Help Restart rollbacks all my root changes (Android 2.2)

[TranceVibes]

Hey guys,

I'm having a lot of fun with my HTC Desire HD (android 2.2).
However there are a few stuff on it that I hate : Stocks application and the noisy startup sound.

Hence as a good geek I decided to install on it Visionary to be able to do root modifications.
I removed successfully the startup sound thanks to Root Explorer and removed Stocks thanks to Uninstaller For Root.

If I shutdown my phone and turn it on, everything is fine : no startup sound and no Stocks anymore.
However if I restart, every root changes are rollbacked : this annoying startup sound and Stocks application are back from hell again!!!

Shall I understand that restart does not really mean shutdown+start?
Is it rather something like factory resetting??? Anyone got an explanation...???

Thanks in advance!