The path in your SSI statement absolutely must be a relative path. Remove the leading slash and use some combination of .. 's to get to your perl script. I have run into this problem several times and it's fairly frustrating!

Update: You must also make sure the file has an .shtml extension, and that you have configured Apache to use the Includes directive on that directory. Test a normal SSI include with --#include virtual="test.html" -- to make sure SSI is working.