Did you ever get this resolved?
The main issue is that the TIOS cannot find 32Kb of contiguous archive memory. Garbage collection attempts to re-locate flash sectors. But... iirc, it cannot re-locate sectors that have been locked. Some programs will lock their files (handles) then forget to unlock them. Or if a program errors out too soon and the handle is left locked.
There is a handle viewing program on Ticalc. It will loop thru every entry in the VAT. I think it will display hidden and locked handles -- which is most likely what your symptom sounds like.
Edit:
HANDLE-Explorer v2.70 by Thomas Nussbaumer
http://www.ticalc.org/archives/files/fileinfo/168/16897.html