I may have pinpointed it but I have to do some more tests...
2 drived were formated as APPLE PARTITION MAP (OS 9 format) and the rest are all GUID - for OS X format.
It rebuilt one drive fine after I deleted the database files, but I have to test an import and capture.
Hopefully I'll have some more time in the next couple of days, but at least it rebuilt that one without any hiccups.
and hopfully this solves the problem! because it is mysterious. and wasn't an issue before 3.5
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