Mike,
Sorry to hear of your difficulties. There is indeed a difference between the CD version of the software and the downloadable version. The CD version provides licensed use of the supplied encoder algorithms to the purchaser of the Phatbox hardware, whereas the downloaded version is time limited. For this reason, regretably, the forum cannot point you to anywhere that you can simply download the software (frankly, I don't know of anywhere either). The problem you will face is that you will also struggle to get any support direct from Phatnoise. Your best bet is to continue to see if your own original can be found, or perhaps to post a message in the Buying and Selling part of the forum.
Good luck,
Les.