It plays perfectly when I just hit the PLAY button - in stereo.

I choose, (ugh, can't remember which menu option it comes from but)...something like "Merge Tracks to Stereo WAV File." There's 3 options in that menu that are almost the same (there's Merge to Compressed File, and Merge Track to WMA/MPA/MP3 or something like that - I pick the FIRST (top) one).

That option is a godsend when it works as I remember back in the day having to do what you describe with the "desctructive" playback/record. Actually I guess I "played" all the tracks and "recorded" onto a new track.
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I think PT does something to initialize the plug ins when doing the fast MERGE thing. It's like it "plays" the song...FAST.

OK, I can deal with the fact the PT and the reverb plugin I have (ReverberateLE) aren't totally great together on the MERGE.

But the stereo is a showstopper as it does this with PG Reverb plug in, too.