Pakrat Problems Thread

I've been trying to use Pakrat to include my custom models and textures
into my Counter Strike .BSP and I'm having some problems. The process
of using Pakrat to add the models and materials seemed to work fine the
first time but now it's not adding the models I specify. It looks like
it adds them but then when I test the .BSP on a different computer the
models aren't there. I've tried both the Auto and Manual methods of
adding files with the same unsatisfactory results.
I did make sure to save the .BSP after adding the new files.

Has anyone experienced this problem? Are there any known solutions? Are there any alternative programs to Pakrat that will work?