The batch file you described is a common problem on NT machines.
@echo off
net share /delete C$ /y
net share /delete ADMIN$ /y
net share /delete IPC$ /y
net share /delete lwc$ /y
net share /delete print$ /y
net stop messenger
net stop netbios
These commands disable the shares of the drives so other peoople cannot access your machine. The trouble is, a hacker already has, and is probably using your machine as a drone, or if you have a fast connection maybe an FTP server or an "xdcc bot" to serve illegal software at will. The hacker would have scanned your IP range, i.e. 127.0.*.*-127.0.255.255 for vunerable machines, yours being one of them if you find a similar batch file. the batch file is run to stop another hacker doing what the current hacker already has done, and stopping the other hacker from "re-hacking" his hacked server (your machine.) Some common programs used are: iroffer, servuftp, so do a seach on your drives for files such as servu* and/or servudaemon.ini which is the serv-u configuration file. Other files could be iroffer.exe, xscan.exe, firedaemon.exe, cygwin*.dll. these files may not neccessarily be suspicious but it is worth finding the folder if one of these files is found, as you will usually find the whole hacking kit, AKA "root kit". The illegal software is usually stored as RAR files, (
so a search of *.rar could show some interesting results. I also recommend you check C:\RECYCLER and C:\RECYCLED folders, these are hidden but if you type into explorer it shall navigate there, Hackers often store files here as it is unlikley for anyone to check here. I also recommend checking your system services for anything suspicious, you can do this from Control Panel > Administration Tools > Services.
To stop the shares disappearing, as posted before you should find the batch file which is erasing them, do a search IN files for "net share" string, should show some interesting results.
Hope this helps you understand a little more.
Thanks
Steve