This would appear to be a possible bug in terms of handling the recent changes in daylight savings rules, with respect to files that were created before the new rules went into effect.
What change of rules do you refer to?
3) I went to look to see if there was an option to make sure only timestamps were being compared (since file sizes change with the different file allocation schemes), and it appears from the documentation that 4.0.7 is no longer supported, as the online documentation applies ONLY to the current BETA version 4.1. Is this Beta version stable? Do I need to upgrade?
File size should not change with different allocation scheme. What is changing is actual space occupied by the file on disk. But this is not the same as file size.
Anyway, by default only timestamps are compared. The criteria can be changed in script in 4.1 beta only. In previous versions it is possible in GUI only. Again refer to the FAQ mentioned before.
There are no changes in timestamp handling in 4.1 beta.