You might be able to help the discovery process along if you zip up your MobileMe OmniFocus.ofocus file after getting one of those errors and send it off to
urgent@omnigroup.com along with an explanation of what you are sending them. My suspicion is that the file is getting clobbered by the MobileMe/iDisk sync mechanism in some fashion. There have been reported cases of the MobileMe/iDisk sync agent getting confused about which version of the file should be kept and asking the user for help; it doesn't seem beyond the realm of possibility that it might (incorrectly) proceed with confidence and squash your data in other cases.
Are you certain that you need the MobileMe/iDisk sync turned on? Do you need it because of the offline access it permits, or do you change the files it contains from multiple computers simultaneously?