That is strange. I've never had this kind of problem with CleanStart. I use it on my TX to prevent most programs from loading at reset (to save dbcache) and for the most part forget about it because it works by itself.
Regarding version, my CleanStart reads as 0.13, which would make it earlier than your 1.0 What's more, this is the first time I've heard of CS 1.0. Perhaps you'd like to test with my version? If so, drop me a PM with your email and I'll send it to you later today.
Also, given that CS is so far the only solution to your original problem, you may want to run a radical test: make a full backup of the E2 (preferably to an SD card using NVBackup or other program), then do a hard reset of the E2. Right after the reset install CleanStart. Do not make a hotsync or restore. Just install CS by other means (i.e. beam it from the TX or the E71, or copy to SD card then transfer to E2's main memory). Don't change CS's configuration. Then connect the E2 to the cradle or USB cable. If it still freezes, then there's some incompatibility within CS and your E2 (which would be the first I've heard). If it does not freeze, then the problem lies with some other program, not with CS. If so, you will have to pinpoint the problem by selectively reinstalling or restoring programs, and testing all the way until you find the culprit. Sounds like a hassle (and it really is), but in the end you will find a solution.