Dreamweaver stuck in endless upload/file transfer when check-in enabled

I'm currently working on a site for a client that has 206 pages and some 2870 files in total (including images, PDFs and some .mp3 and .wav files).
The client works on the site in Contribute. This is a site I initially created 5 years ago - I'm doing a massive update for them (new templates, new CSS etc.) After I'd done some of the updates, I turned on check-in/check-out and re-checked the Contribute compatibility checkbox etc. in Manage Sites.
DW started marking the files as checked out (or locked, if I hadn't downloaded them recently) etc. - as I would expect it to do.
Except it kept doing it - for hours and hours. I couldn't do very much while it was doing this - everything in the menus became almost non-responsive, and I certainly couldn't check pages locally (I have MAMP installed - the pages have some PHP)
I finally let it run over night.
It was STILL transferring files in the morning! I started watching the FTP window - and it would appear that certain blocks of files were being transferred over and over.
I finally just hit "disconnect from remote host" - and have had to do that anywhere from 5-10 times before it actually breaks the connection.
Every time I reconnect to the server, it starts all over again - it will just keep transferring files forever. It keeps doing this, even though almost all the files are marked as checked out, or checked in/locked. I say "almost" - there are some it just never seems to get to. I've tried changing FTP settings (passive/not), tried deleting all the remote settings and then putting them in again. I tried deleting the _mm folder off the server in case it was corrupt. Nothing worked.
I finally just turned off check in/check out and that is the only thing that stops this behavior.
Any suggestions on how I can fix this so I can I get my work done and have my clients up and running again on Contribute? I haven't tried dumping .plists yet, and have also considered just taking everything off the server and re-uploading the entire site.

Thanks, Elizabeth.
I had been putting the updated pages for the site in a Test folder, but since I've now got 150 of the 206 pages on the new template (and the remainder are in an archive section of the site - one of my clients is a bit of a squirrel ) and the school year began 2 days ago, they were eager to get the new version of the site up and running, so it was all uploaded on Monday night. (It's a public school organization - SpEd and Enrichment services for a chunk of northeastern MA)
For the time being, until I get a little farther, I'll leave check-in disabled, then before I re-enable it, I'll clean off the remote server and start fresh. And cross my fingers. I'll let you know how that works out, just in case anyone else runs into the same issue.
If anyone has any further suggestions or experience with this sort of odd behavior, let me know.

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