You have breadcrumbs in your popups. (Sounds like a breakfast problem, doesn't it?)
I think this is what's going on. Either you turned on breadcrumbs for all your topics during generation, or you added breadcrumbs to a master page (i.e. template) that is used by your popup topics. This may have happened if you added breadcrumbs to your standard topic template and didn't realize that the popup topics use the same template.
If this is the problem, the easy fix is to create a new master page with no breadcrumbs and apply it to all the popup topics. You should be able to select multiple topics and apply the master page to them all together (I know you can do that from the Topics panel in RH6).
If this isn't the problem, there may be something going around in RH8 - you're certainly not the only person who has posted about conversion and breadcrumbs.
Post back and let us know. I'm eager to find out - I get to upgrade from RH6 to RH8 this month.
I did turn on breadcrumbs at generation time. Then I tried going back and turning it off and it still produced the same problem with the new help system. How do I get breadcrumb placeholders off my few pop-up topics? I created a new master page and it doesn't show any breadcrumb placeholders and I applied it to one of my pop-up topics to test it. When I previewed it, it still doesn't display correctly. Not sure what to do now?
After much trial and error testing around this image map issue, I cannot seem to find a fix for image maps within RoboHelp 8. No matter what I've tried (and it was a lot), nothing seems to fix the image map problem. Even creating a new image map on a new page with totally different info, pop up pages, image, etc. and turning OFF all breadcrumbs - the image map does not display correctly once generated (nor in preview).
I have found a VERY TEDIOUS workaround for this (that I'm not happy about). If I take my original pop-up topic htm pages (9 of them) from my RoboHelp 6 project and the original eHlpDhtm.js file from RH6 and place them in my output Help file from RH8 (overwriting the RH8 with the RH6 files), then the image map works correctly.
The eHlpDhtm.js file has many more scripts in it than just the image map triggers, so I'm not sure what all else I'm affecting when I'm fixing one problem (i.e. not sure how many more problems I'm creating at the same time when fixing one problem.)
It's almost like the "breadcrumbs" feature in RH8 has broken the image maps feature in RH8.
I'm still up for more suggestions as how to fix this if anyone has any ideas.
This is probably a day late and a dollar short, but I've just upgraded from RoboHelp 2000 to RH 8 (woot!) and I had the same problem for the longest time, and this is how I solved it:
Call up the Single Source Layout pod. Select what you want as your Primary Layout (for me, it was WebHelp). Right-click and choose Properties. Click "Next >" at the bottom. On that page, under Navigation, uncheck the "Add Breadcrumbs Links" box. Click Save.
After I did that and re-generated my project, the breadcrumbs were gone. I hope that helps!