I think i have an answer to one of the problems.
If your using the LK version of this hack, the control panel section updates the vars_modifications.cgi file with the save to location BUT the upload.cgi code reads the save to location from the vars_misc.cgi.
I had this hack installed on my old 6.1.05 ubb so the vars_misc.cgi locations were carried over and i get an invalid folder error but if you havnt installed this before there will be no locations stored and I have no idea what error it will give...
Also theres a 5 on the end of the #!/usr/bin/perl line, on my ubb it wont do anything unless i remove it.
Anyway hope this helps (if i am right that is)
Forgot to ask, which is the best way to fix it, edit the mod or edit the upload.cgi?
Paul