Sorry, but my Cougar is i nstalled and running in my car so I can't check anything. All I can suggest is that you stick in some debugging code such as pick a point early on in the program and turn on (or off) a led or something so you can see if the program gets that far. If you can get that to happen, then keep moving your code along to where it doesn't work.
Its not a bad idea to write a little subroutine to turn a led on, wait a bit and turn it off, then you can just put in a call at various points.
That's about all I can suggest, maybe someone else has a setup closer to what you are doing and can help?
For what it is worth PonyProg can be downloaded here
PonyProg - Serial device programmer and the serial interface is just a converter from RS232 to the Atmel ISP logic levels. It'll work with just about any hex file but needs a COM port - doesn't work with USB.
Just an afterthought: if your own code works OK and you say it does, it must be something in the Cougar code that is not compatible with your setup, so the debugging idea will be the way to go.