I'm going by memory here as it's been over a year using the old controller system, and make suggestions that may point you in the correct direction. I may be vague only because I'm going by memory. Hopefully others will chime in with more.
Are you using MPLAB 7.2? There is a special version of MPLAB for the FRC robots that has all the libraries etc you need.
Actually, first off, are you using Windows XP, 98, or Vista?
The FRC_MASTER_V13.BIN file just loads the master code for the robot controller and does nothing for "driving" the robot.
.hex files are what you want to download to the robot. The FRC_Default.hex is probably very
very basic. Anything you compile with MPLab turns into a .hex file.
There might have to be some tweaking with IFI_Loader on which serial port you need. I seem to recall a menu for that.
There is also the "programming button" on the robot's controller that must be pressed prior to downloading. Press it only long enough for the lights on the controller to change -- much longer and you get the "christmas lights" effect [blinky lights] which you don't what it to do. It sounds like you got that part okay.
There is a website by
Kevin Watson that you might want to look at. He rewrote the IFI code for FRC specific items. You may have to go to the 2007 page for less experimental code. For 2008 he wrote a very clean version of the robot code that had very little of the original IFI code.
Remembering the old controller setup might be a good idea, at least until all our old robots give up the ghost. Good luck!