Yes, my apologies. It turns out I was using an old version of CGI.pm Upgraded and unearthed the upload() function.
Just trolled the apache error logs and can see an error message being generated from mod_perl:

[client xxx.xx.xxx.xxx] Request content-length of 84482 is 
larger than the configured limit of 75000
[download]

Which probably explains my problem with file upload size :)
Thanks a lot for your help.

*a bit later* Turns out this:

LimitRequestBody 75000
[download]

was in my httpd.conf file! *slaps forehead*