This are symptoms of TOS 1.02 . I experienced such in similar case, when partition was near to be full with data.
With TOS 1.02 file count limit is about 16000 per partition (at least in theory), so it is not problem for sure. I tried to add FOLDER100 to driver, but it did not make it more reliable. TOS 1.02 is simply not good enough with hard disks. Upgrading to 1.04 is best what you can do. What can do at moment is to spread games on multiple partitions, and not filling them over some 60% .
Famous Schrodinger's cat hypothetical experiment says that cat is dead or alive until we open box and see condition of poor animal, which deserved better logic. Cat is always in some certain state - regardless from is observer able or not to see what the state is.