I too have noticed that where "Merge into Background" seemed to override everything in previous versions, now transition pop-ups seem to still appear at the end of a slide over a merged image. Two practices I've found helps:
- Make sure you keep the clicks you capture a clean as possible with recording. If in doubt, I capture an extra screen shot as a back-up and then simply replace the background image on the slide I need it, or delete it if no longer needed. This practice is often faster than trying to doctor screens using the "Merge into Background" feature. Also, I'll often just extend the image to the end of the slide (rather than merging) and it gives me more control of all pieces should I need to change directions later.
- I think your SWF Quality Preferences may aggravating the issue too. I've found these settings to be more reliable that the defaults and still keeps file sizes managable for most projects.
(Increase the Jpg % if needed to 100%, then if that fixes the issue, you can back off the % to save on your file size / bandwidth... This link/discussion may be helpful: http://forums.adobe.com/message/5264641#5264641)
Let me know if this helps!