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Well, that one is a bit of a stumper. Here's why.
First off, I tend to think of a mythological Roman God named Janus when I thnk of Master Pages in RoboHelp. Here's why.
Janus was the God of Beginnings and Transitions.
One way Master Pages are used is to Begin a topic. (Janus as a Beginning) A topic template. As you create a topic, all elements of a Master Page are dutifully copied into the new version. You then modify the new topic by changing what is inside the Body placeholder. At that point, there is no connection between the Master Page and Topic as far as the Body placeholder goes. You rearrange the Master Page and no topic created from it follows suit.
The other way Master Pages are used is to influence changes to existing topics. (Janus as Transitions) By defining a Header and/or Footer, you then associate the Master Page with many topics so that the Header and/or Footer populate across the existing topics. And subsequent changes to the Master Page Header or Footer *WILL* populate across any topic associated.
There is what I refer to as a "no man's land" area with Master Pages. Content you place in an area that isn't the Header or Footer proper but is outside the bounds of the Body Placeholder. And it's been my experience that this too will populate as the Header and Footer will. Sounds like you are using this.
Certainly you can try inserting the CBT code in the HTML. It *MAY* accomplish the goal. But I might think a simpler solution would be to define a separate Master Page used for Print purposes. Then select all the topics in the Topic panel and associate the new Master Page with them and generate the Printed Output.
Cheers... Rick 
As Rick has pointed out, a master page has three elements, header, footer and body. There is also the no man's land that can reasonably be argued to be an undocumented feature and if you use undocumented features, you cannot really complain if things go wrong. My understanding is that you are creating a table and then putting master page elements inside and outside of that. Unless I am not visualising what you are doing correctly, that's not how they are supposed to work. You put things is the defined master page areas, not put the areas into a table.
Rick has suggested a simple solution. In the topic list select all topics and then in one action, select a different master page that gives you what you want. How difficult is that? Of course do it with a copy of the project first time around.
The simple fact is that master pages are intended to give a header and footer in online help and default content for new topics. Changes to the header and footer will apply to all topics, changes to the body will only affect new topics associated with the master page, not existing topics.
Anything in the header and footer of a master page doesn't go into print so I think using master pages how they were intended to be used would give you what you want.
You talked about putting the body placeholder in a cell but I am not seeing a reference to a nested table. I have plenty of nested tables that work just fine in print.
Instead of having a pop at the developers and telling Rick his ideas are insane, which is odd given he is the longest serving supporter of these forums, perhaps explaining why they don't work for you would be more productive.
See www.grainge.org for RoboHelp and Authoring tips
You talked about putting the body placeholder in a cell but I am not seeing a reference to a nested table. I have plenty of nested tables that work just fine in print.
The idea that nested tables don't work very well in print (or tables with merged cells) came from this page.
telling Rick his ideas are insane
His ideas aren't insane: the fact that such workarounds are necessary is insane. If I can right-click to apply a conditional build tag to a topic, why not to a master page? Why not to the body placeholder, when I can with the other place holders? Why can't I apply the tag to everything BUT the body placeholder? I can do it on a topic page with the Topic TOC placeholder.
if you use undocumented features,
The Master pages document for RH 10 says "You can use tables to create a precise layout where each placeholder is placed in a table cell."
The Master pages document for RH 8 shows the following image:
I assume that the "Layout Area" is this no-man's land?
This Layout area is like any other Editor area where HTML content may be placed. The difference with the content outside Body Placeholder i.e. the Layout area is that these contents are not shown in the associated topic but are patched during preview/output. RoboHelp 8 overrides all layout settings (e.g. Borders and Shading Properties, Background Color etc) of attached Topic from that of the Master page.
Given such documentation, I'm not sure why my complaint falls under "if you use undocumented features, you cannot really complain if things go wrong."
Yes, I'm snippy about this. It's inconceivable to me that a product 10 versions in would require so many workarounds and have so many oddities and inconsistencies and require so much outside consultation in addition to the user docs. I don't like being thwarted by stuff that doesn't work in a sensible way. The SW developers I work with would rather dig out their eyes with a spork than push something like that out the door.
What my page says is
This does not mean that you cannot nest tables and print, just that if you have a problem, then consider this as a cause.
On merged cells the page just explains how they work.
Maybe your are frustrated by this but that is not the fault of Rick or myself who are trying to help you. If you want to keep blaming Rh for the problem before we have found out the cause, then good luck in resolving this. I prefer to find out the cause first and then attribute blame. At this stage, tt might be Rh, it might not.
If you want to work with us, then can you give me a link to where that image is shown? The help pages I looked at for Rh8 don't have an image in and when I create a new master page in Rh8 or Rh10 it just shows the centre area, same as in Rh10. You can use tables within that area or you can use tables above and below but you cannot change the way master pages work. From what I can make out that is what you are doing.
If you want to create a new project using your master page and a topic to illustrate the problem, I will take a look. See the Contact page on my site. Make sure you explain what it is you don't want to see in print and include a link to this thread.
See www.grainge.org for RoboHelp and Authoring tips
I am using TCS4 (FM11 and RH10).
I have a project where my FrameMaker book is linked by reference into RoboHelp.
My FrameMaker content uses 'Conditional Text'. RoboHelp seems to pick up on this automatically, tagging that text with a corresponding 'Conditional Build Tag' in the RoboHelp project. (This is good!
There's one thing that's annoying me, though: in FM, by Conditional Text tag is set to colour the text Red. In RoboHelp, it changes this into a red dialogonal hatching behind the text. I'd prefer it to keep the text red, the same as it is in FrameMaker (because the problem is, my primary outout from RH is a .CHM file, and there is no formatting at all applied to the conditional text in the .CHM output).
Is there no way to do this?
It looks like I am going to have to apply Conditional Text and a dedicated red Character Format in FrameMaker, to have this text automatically appear red in the .CHM.
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