[Hampshire] FAT32 problems

I have written a data logging programme which stores data on an 8GB USB
drive and has worked without problem for some time until disk access to
the drive became more and more sluggish (files were deleted and so the
number at any time was no bigger that 100). The hardware is a National
Instruments cRio, VxWorks OS.
The only possible problem that I discovered is a warning in
documentation is that the file system is FAT and filenames should be
limited to the 8.3 format. I wasn't aware of that and used filenames 14
characters long.

The problem only shows itself when using FTP to list files. It seems
that data transfer is OK from the USB drive. It looks as if the system
drive is OK for all FTP operations.

I suppose I will have to change the software to conform to the 8.3 limit
but I am not at all confident that this is the root of the problem
since the datalogging software seems to work well and it has taken a
long time for problem to emerge. Another worry is that by having used
the illegal filename size, somehow the structure of the disk has been
changed and it may have to be reformatted.

Can anybody throw light on this.

Thanks

Roger