Sig 3161 (MKD overflow) triggered for one of my customers when he was replacing some cgi scripts. From NSDB:
This signature triggers when an attempt is detected to create or delete a directory during a FTP session using a path argument containing executable machine code, also know as shellcode. Subsig 0 watches for use of FTP 'MKD' command with shellcode in the path argument. Subsig 1 watches for use of the FTP 'DELE' command with shellcode in the path argument.
Is it possible that it is interpreting certain cgi filenames as shellcode simply because they are named similar to shellcode?