Did you solve this yet?
There are 2 directories that take items that are executed on startup of FrameMaker: both are called startup. One is in the FrameMaker program directory, the other is user-specific and is located in the <User> \ AppData \ Roaming \ Adobe \ FrameMaker \ <version> directory.
Check both directories to see if the script was installed in either one. The Script Catalog dialog in FM11 does not have an 'Install on startup' option but there is a Move to Autorun button, which copies the script into the user-specific startup directory. If the script came with an installer, it might be moving the script into the program startup directory instead.
If the script keeps appearing and it is not in either startup directory, you should be more elaborate about the type of script, the exact method of installation and uninstallation, etc. I am just going by the short info you are giving, which might be about another type of script altogether.