That is so strange. I use a 3329 based module as well, but the 3339 is supposed to be functionally identical. There's no reason to change modules if yours works with the MiniGPS program, I was just making a comment.
Try setting up the module for 57600 baudrate, GGA: 1, RMC:1 (all others:0), DGPS doesn't matter, and 5hz fix update rate through the Mini GPS program. Another possibility, is it at all possible that your RX and TX wires to the GPS are swapped? (I have problems with this all the time.)
That's the best I can come up with at the moment, sorry and best of luck.
Ooohh! something else that may or may not be worth a try is changing that line of code to: