It are the ones that are automatically generated by the Backup preference in OmniFocus. And they also contain 1 xml file in the format you explained.
The only difference I see is that the format of the xml file in my local backups has a forward slash in the name, e.g.
root=79FC2B55-EF4D-4FE4-B679-D5A9B470BB9F/8C7F963A-56FE-4AA1-999A-3DE656027843.xml
whereas the name of the xml file in the remote backups don't have the slash, e.g.
root=166009EC-E05A-4407-A744-B02C5B356FCF5B376110-2E51-4B99-9521-CECC67987E46.xml
Maybe it was converted during the backup? Anyway, the local backups restore without problems, the remote ones don't work.
Manually adding the forward slash doesn't seem to help either.. However, when looking at the same files in terminal, it was a colon ':' instead of a slash '/'. Adding a colon at the correct position seemed to do the trick.
So apparently the ':' in the name of the internal xml file is lost during backup via Mozy. Putting it back (after the twelfth character of the longest string) fixes it.