OK, there's another user who's reporting a similar problem, so let's try to get the same information in-house from you:
Could you provide me with a listing of the "root" directory of this drive, when Time Machine is OK with it, using:
in Terminal (that's LS -LA in lower case). Then, run SD! and do the same thing again once TM starts complaining.
Send the results of both to me at the support email address.