Question: Have you ever modified your default /bin/ro, rom, rw, rwm commands?

Reason: (And this one will be a trifle obscure, so be patient with me...) On the large disks, when you manually execute any of the mount commands that are default in the player distribution, there is a "mini-diskcheck" that is basically useless, but time consuming. You may note that doing a "rwm" command from the shell may take upwards of a minute (subjective time) to complete. This is because the command as written does not have the "nocheck" option built into it. For example:

rwm unmodified:
#!/bin/sh
mount -n -o remount,rw /drive0
[ -e /proc/ide/hdb ] && mount -n -o remount,rw /drive1

rwm modified:
#!/bin/sh
mount -n -o remount,rw,nocheck /drive0
[ -e /proc/ide/hdb ] && mount -n -o remount,rw,nocheck /drive1

I think I had this problem long, long ago, but I have been running with modified ro,rom,rw,rwm files for so long, I no longer remember. This may have fixed the problem.

Now, I do not know exactly how the ftp daemon / kernel implementation is changing the mount status, but it is certainly possible that your player is being powered off or quitting to shell before the change in mount status completes.

An interesting test would be to sit on the shell while all of this is happening. After your script completes, see if the partition is still read / write, if it is in the process of changing mount state or if it is read only.

Also, capture a boot after executing that batch. Capture also going into the shell and doing a "rw" and "rwm" command. Whatever file system is "dirty" will be flagged in the error messages on console, along with the text of the error.