Greetings!

I've had to do something similar, though not with Laserfiche.  We have a good number of virtual desktops, though with our setup most users get the same machine over and over, and have their profiles redirected.

In some test pools we use, though, we do have nonpersistent virtual desktops.  In those cases the machines are wiped on logout.

In one case we had an old app which stored its settings in a folder on c:.

For this app, we set up a .BAT for the users to use when using this app.  We added some error detection, etc, but the basics were:

1. Copy all config files from <user's network share> to config folder on C:
2. start the app
3. Copy all config file back to <user's network share>

So... in this case, I'd set up a script or two to copy whatever you need - files, registry settings, etc - for the scan settings off to a user's share.  Set one script at login, one at logoff to copy the files back.

It's a bit of a hack, but should take care of it.