Kostya,
Thanks for the reply. I was basically stepping down the list of emails individually. I would open up an email, move it to a folder, then the next email would automatically open, and I'd move it to the same or different folder. Occasionally, I would mark an email "unread" and then I'd be sent out to the Inbox list. I'd then open up another email, and do more moves on a bunch of emails. I would say that I was moving a total of 15 emails, with a move command about every 5 seconds. Of those 15 emails, only 2 didn't really go into the folders (i.e. Aquamail showed them in the folder but Gmail showed them in the Inbox still.)
I have noticed that once the issue starts - i.e. the move works on Aquamail but Gmail doesn't show the move (i.e. email still in Inbox) - then I can get it to happen again easily if I start moving lots of emails around. However, if I then delete the acct in Aquamail and recreate it, this issue stops happening, even if I use the same bunch of emails. Last time, after I recreated the email acct, Aquamail took 3-4 weeks before this behavior happened again. Lots of folder moves worked perfectly. Then something changes somehow, and the issue starts happening here and there. The emails are new obviously but the folders are the same ones that had been around the whole time.
Annemarie