The file times should not be getting changed. We use Backup APIs to rebalance and call SetFileTime to prevent the time shift, as documented here:
http://msdn.microsoft.com/en-us/library/windows/desktop/ms724933(v=vs.85).aspx
"To prevent file operations using the given handle from modifying the last access time, call SetFileTime immediately after opening the file handle and pass a FILETIME structure whose dwLowDateTime and dwHighDateTime members are both set to 0xFFFFFFFF."
This is exactly what we do and it prevents the file times from being modified.
For directories, we have a setting called CoveFs_SynchronizeDirectoryTimes, which is on by default in both 1.X and 2.X and is meant to synchronize directory times after a clone which happens after a rebalance.
In theory, 3rd party apps can change directory times. If this can be reproduced without any 3rd party apps then this should be classified as a Bug.