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This still sounds like a problem with the window name(s). What is the [WINDOWS] sections in the projects' HHP look like?
I had the window names set correctly, but one of the projects was compiled with the default window! I re-compiled and everything worked great.
I'm sure I'll have more questions as I get further into this, but thanks for all the help thus far.
Possibly not relevant to your current issue Aaron but...
as a matter of fact, there are occasionally situations when a message of the form "”The window name “xxxxxx” passed to HH_GET_WIN_TYPE has not been specified" appears even when you have set all your window definitions correctly. This happens when you use the "Related Topics" command to call a topic in an external CHM and you specify a secondary window name. Strangely, the message only appears if you have MS HTML Help Workshop installed on your computer, so it is probably not an issue for the average user. I believe it is an HTML Help bug.
Matthew and Dirk are certainly pointing in the right direction. Microsoft never got around to squashing all the bugs in MS HTML Help. If you are working with secondary windows I highly recommend prefixing all window type names with "$GLOBAL_". I always do that as standard practice as it was recommended by Microsoft's lead developer of the .chm format, Ralph Walden. You can easily do this in RoboHelp's Window Properties dialog. So if your window name is "Secondary_Window" you would rename it "$GLOBAL_Secondary_Window". I put the prefix on all window names for good measure.
For more info, try Rob Chandler's site http://www.helpware.net/htmlhelp/how_to_merge.htm
Click on the link "Secondary Windows" for the good parts.
One final thing, you probably already have, but be sure to download the latest service release so that your version should read X5.0.2. Updates are here: http://www.adobe.com/support/robohelp/downloads.html
Hope this helps.