Could CompareIt! consider these files as read-only (and override the "Do not edit read-only files" to YES) instead of aborting with the "Failed to read source file!" message?
I frequently find myself text comparing files saved from Word, and I have to close the file in Word first, compare, then re-open the file in Word. Such files can be opened as read-only by other applications such as ExamDiff Pro.
Hope that helps,
Dan Dascalescu