Take a look at foldit.bat. In particular the line that invokes foldtrajlite.exe should have a -it in it. If it has -if (internet false), it will never attempt to upload. Not certain what the default is, since I always set my flags true or false explicitly.
Also take a look at your error log....
It wouldn't be a bad idea to set the -qf flag (== quiet false) and run the program and watch - look at what the console is saying as the program comes up....