Logic 9 Merge behavior

Hey folks, I'm a late upgrader to Logic 9, so sorry if this is a newbie question. I'm having an issue with the merge function in 9 that I didn't seem to have in 8.

I'm in the habit of editing regions into small sections (manually "gating" toms via transient edit or strip silence). I don't like dealing with those tiny regions, and in 8 would just select them and MERGE. I'd get the "continous file" warning and hit OK. The regions would be merged with the gaps I'd edited in.

Now in 9 I do the same thing. If I do the same process, there is no warning and the regions get merged back, with the material I'd edited out returned. Not what I wanted. Only if I add fades to the end and starts of the regions does it behave the way I'm used to.

I've obviously missing something in the manual, and know there are new bounce/merge features with a right click. They aren't seeming to do what I want. I'm not wanting to "print" my effects or move the merge to another track. Just want to consolidate the regions to new audio files with the edits. Am I doing something wrong? Preference or Inspector check box I've missed? User idiocy?

Thanks for any help you can give me.