It depends on what checkboxes are set when doing the cleanup.
The svn library has problems with some combinations of the flags.
Thanks for the hint. Maybe this helps to trace the thing down if/once I get to check it out.
FTR: As far as I recall the dev explicitly tested to only have
the "Clean up working copy status" setting in the dialog ticked:

I asked him to double check this next time. Unless I'm getting
back on this, then this was actually the case.