Could you enable verbose logging (under Rules Manager... Options... Advanced...) and send me the log file next time this happens please? You can access the log file from Rules Manager...Statistics... then click View Log... You can then submit it here (upload via your user profile then post here to let me know) or email it to me.
v2 of Rules Manager is very close to completion. It has huge performance enhancements as large parts have been rewritten using Extended MAPI, and it has been tested against Vista, Windows 7 and Exchange with a huge number of folders and items.