I'm having this problem too, on XP professional. Trying to run any batch file from Windows file explorer (or xplorer2, my two-pane replacement) crashes the explorer. So does trying to run cmd.exe from the explorer. In addition, the taskbar goes away for a few moments, then regenerates itself. Running cmd.exe or regedit from the run command line in Start has the same effect.
As Charybdis suggested, I scanned for cmd.com in c:\WINDOWS and found three instances: C:\WINDOWS\$NtServicePackUninstall$\cmd.exe, C:\WINDOWS\ServicePackFiles\i386\cmd.exe, and C:\WINDOWS\system32\cmd.exe. The lengths and checksums (computed by xplorer2) show that the last two are the same. The crash happens when I run C:\WINDOWS\system32\cmd.exe directly from this location.
I've got another XP Pro system, same update level, and its copy of C:\WINDOWS\system32\cmd.exe, which behaves just fine, has the same length, date, and checksum as the one that crashes file explorer on the bad machine. If my cmd.exe is bad, someone did a very careful job of hiding their steps! In fact, like bfasula, I tried renaming the file and running it, and it works just fine. So it's not the series of bytes in the file that's at fault.
Actually, that's not exactly what bfasula did--I renamed rather than copied, and as a result when I ran it, there was no cmd.exe in c:\WINDOWS\system32. But when I exited from the DOS window that my renamed copy (cmd1.exe) opened, lo and behold, a new cmd.exe appeared right along side it in my explorer, and when I tried to run that, it misbehaved as before.
I'll be grateful for any help that anyone can give!