I know it may seem counter productive, but:
The design sounds fairly simple. Excuse me for glossing things over. That's not my intentions. But 8 channels of switched "high-tech FX" doesn't sound like terribly complicated. Regardless, it still sucks to have to start over. And having said that, have you bothered to simply trash your existing show(or move it somewhere else) and simply start over?
Seems you're not the only one recently having these sort of problems. I had these idiots when I was starting off and I simply trashed my show. My show only had my lights properly set up on their channels and maybe at that point in time only 8-10 scenes of color washes using my 64LED Pros. Lucky for me, I wasn't missing much.
But, this is why I also recommend that people who HAVE controllers DO NOT give them up yet. While MyDMX has been pretty solid for me, I don't trust it 100%. I'm an old school hardware-based guy, mainly for audio, but it applies to my ideas on lighting, and while all the touring audio guys I work with pretty much use consoles for lighting exclusively. But, then again, we have to consider that this is what these people do for a living, so the mindset is different.
While "MyDMX" is my go-to for lighting, my DMX Operator is super close by and ready to be switched to(except for the fact I have nothing decent programmed into it). It will work, but it sure won't be pretty!
Also, since I'm posting, please ensure you're using the latest release of MyDMX, which I think is dated June 8 2008. It may address the problem. It's worth a shot as well.