I can think of 3, maybe 4 possible causes.
1) You haven't set max transfer rate of the drive to 0X1FE00 in Hard Disk Toolbox (necessary to limit data length in a single transfer, it doesn't affect speed).
2) The Fast File System. This is notorious for "validating", ie detected a problem with the hard disk and spending hours and days trying to fix it. The best solution is to update the file system to PFS3AIO filesystem on the drive, which meanS copying that filesystem it your HDToolbox floppy and starting from scratch on making partitions.
Part of the problem here is the way that FFs updates a file - it can open a new copy of the file, but fail to save any data to it, which is why you get a file length of -4 on the newly created file. PFs3 makes a whole new file, deletes the old one, then renames the new one, which is a much safer way of changing an existing file.
3) Malware causing a fake file to be written to the hard drive. Do you run a virus checker at all?
The other thing could be using Kickstart 3 Rom with that accelrator. It's not ideal because you have to add most of the memory after Workbench has started. Unlikely to be that in this case.
EDIT: Kind of useful if you are trying to do 1 and 2, look up these;-
https://www.youtube.com/watch?v=tL8etprxj4Ehttps://www.youtube.com/watch?v=ckL5xYQjqLo