You probably extracted a couple of files from the PlugY incorrectly. Also, Atma and Median don't get along well together. Remember not to accidentally load M'08 characters or any XL characters from before the .21 patch; those too were wiped. Also remember that all of the .dll files are the correct ones for the patch; you might possibly be using the 1.12 modified d2gfx.dll to run multiple instances when you should be using 1.10's modified.
If you already have 1.12 and did all of the necessary things to make it run without the CD, then just save a copy of the original d2_patch file into a folder somewhere, and copy/paste the Median XL's version. Otherwise, if you need anything from the CD, such as running the game from any version pre-1.12, or you didn't copy the right files over after you upgraded to 1.12, you might be done for. Alternatively, you can register your CD Key online with Blizzard, and they'll give you the patch; then again, you'll still run into the problem of needing CD files (unless Blizzard also offers the requisite files).
Apparently, Druids and Charm got a massive buff recently. Additionally, PlugY is dead with 1.12. Be forewarned.