"...check for a script that contains a subfolder of support script files. the older version of the script lloyd referenced had something like 1000 files in a subfolder, but an updated version seems to have fixed it (by enclosing the folder in parentheses). also follow aliases/shortcuts to other folders."
Update: in a comment below, Jeff provides a hard limit for AE CS4 9.0.2 -- 898 on Windows and 897 on Mac. Jeff is also the author of Additional Scripts for After Effects CS4 which includes Launch Pad, which creates a docking panel to run other installed scripts.