This bug was actually not my fault. If you find a copy of the original 3.5 runonly from GFA it should produce the same bug! When Frank built the runonly and removed parts of the editor he introduces new bugs. Since there was no 3.6 runonly I used the 3.5 version as a guide to build mine and ended up duplicating his bugs.
For those that do not know GFA incorporates a 4kb read/write disk caching scheme. You can verify this by reading a byte from a file, pause, then read another byte and the drive LED will not blink on further reads until you exceed 4096 bytes read. It's somewhat redundant under MiNT since MiNT has its own disk caching scheme, but its never caused any problems. The caching scheme is so intertwined in the file I/O code that I am afraid to remove it, so it remains unchanged. It does make it extremely fast on plain TOS, so its all good. Anyway the above bug, was a missing call to flush the disk cache before the files were closed. I thought you would like some background info on how gfa works internally.