I don't think it was the Task29 tool that is messing with your phone. I had it happen on a couple of ROMs I've built before Task29. I think the SYS had more to do with it, but many people think it might be the radio. I'm having more luck now that I am remembering to run "clear storage" each time after I flash.
I still have the new Sprint radio. I change my ROM a lot. I just cross my fingers and reflash when I have an issue.
Good luck.