help after Dual Boot program went Wrong

i'm haveing a problem in win98 forum heres the link http://discussions.virtualdr.com/For...ML/047328.html

Heres the jist of it:

when i restore my ghost backup of win2000 install...then reboot it.....it startsup and when in windows i get 3 explorer windows then it says "windows 2000 has finished installing new devices. You must restart your computer before the new settings will take effect", "Do you want to restart your computer now?".....

....after i restart it it seems normal......i havent added any new devices, what the hell is it on about, is it detecting changes in my MBR or sumut? do i need to be concerened about this?....really i want my PC back to how it was b4 i installed this damn BOOT Manager.

Another Question, if i remove all partitions with FDISK, will this also remove my MBR if not would it the be safe to FDISK /MBR.
I backup so i can return my PC to a previous state after a disaster, why is this giving me grief....should i have backed up my MBR as well?

normally when i reghost it doesn't do this, any ideas please https://discussions.virtualdr.com/

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HP Pavilion 8730uk: Athlon 850, 512mbRAM, TNT2 Pro, SB Live1024, Win98FE/2000Pro & Cable Modem.
LG CED-8083b CD-RW, Samsung SD-612 DVD-ROM, Quantum 30gb lct15-30 & Western Digital 45gb WD450AA HDD