Hi Kirk,
Seeing you're already changing crop behaviour in the latest beta, this might be a moot point but I thought I'd share my experience from this morning anyway.
I ingested a shoot (1000+ images of an event) with PM but forgot to add a bunch of IPTC data during ingestion. Went over to LR3 beta2 for postprocessing and along the way changed crop and rotation for quite a few shots. Just before exporting from LR I noticed I'd forgotten to add some IPTC data to all files and went back to PM to correct this mistake and wrote everything to both RAW and XMP. I then in LR gave the command to reread metadata from saved xmp files, thinking PM would have only added IPTC info. Wrong assumption... On every rotated image, both crop and rotation settings had vanished. Luckily I had a backup so everything was solved quickly. Somehow PM, at least in its current non-beta version, messes up crop AND rotation changes in XMP, at least in LR3 beta2 sidecars.
Just thought I'd give you this bit of info. As stated: it might have been addressed already, I don't know as I didn't download your latest beta.
Cheers & have a great weekend!
- Emile