Windows 98 and filenames

Ok, this is bugging me now.

My family owned a network drive (piece of hardware, basically a small linux box that has a shared folder), but the fan went kaput and the drive refused to operate. We dismantled it, backed-up the data, and reassembled it, and sent it off for a new one, with a note saying the data was fine. (Duh, we'd just backed it up...) The company, of course, merely sends back a new one - they didn't transfer a single byte. (Good thing we backed up.)

The Problem, however, is that we just copied the files. We did this on a Windows PC, moving the data from an ext2fs drive to a NTFS one, and then back again on the new drive. The data itself appears to be fine. But the directory structure seems to have become a little queer since then.

The drive, to me (the Win98 box), is mounted as a network share on N:\. Skulltag was giving me issues before - the launcher was complaining that the exe didn't exist. (Even though it did.) So I wrote another launcher, stored it in a folder off the root (which has no spaces and is <8 characters) and pointed the first launcher to that laucher with then launched Skulltag. (A kludge if the world has ever seen one.) Problem "fixed".

Now, I start MySQL for the first time in decades. (Ok, since the drive failed.) It doesn't start, giving a "Can't find messagefile 'N:\Program Files\MySQL\share\english\errmsg.sys', aborting." message. If I directly copy/paste the filename into Textpad/Notepad/etc, it open right up. I uninstalled MySQL (it was version 4.0) and upgraded to v5.0 in the hope that it would be fixed. I hoped in vain.

Here's the questions: Any guesses on what sort of bad mojo these programs are performing on the filenames? Also, I suspect either long->short filename conversion or long filenames (or filenames with spaces) (or all of the above): Where does Windows store the short filenames? (There seem to be no special files in N:\ or N:\Program Files) Any ideas how to fix?

Sorry for the long explanation, thanks in advance for any help.
EDIT: And if you're wondering why I store programs on a network drive: It workes fairly well (up until now) and C:\ has <8GB. N:\ has >150GB.

The command of the day is
dir /x

One problem I can think of if you're relying on short names in some way is that if you copy long names to a new volume, the equivalent short name can change.

For names which need contracting, you end up with xxxxxx~n type names, but the ~n is a rather dynamic thing in that n increments with every new short name generated.

dir /x gives "Invalid switch" on my PC. Could be due to Win98. (Googled it. Win98, AFAIK, always shows short file names.)

I'm not sure anymore if short filenames are the problem - MySQL's ini file has the full pathname. I'm still curious as to where Windows keeps these filenames. Generally, yes, it's xxxxxx~n, but this drive has always had odd ones. Program Files is "PROGR~-I", Mozilla Firefox is "MOZIL~6H".