Update,
I finally solve the problem with the information provided by elroy.
It was a Trojan that created the problem but the fix was everything but easy.
I was not able to format using a bootdisk, the partition was in NTFS. I have Partition Magic so i use it and created 2 partitions that i formated in FAT 32. I was able to use fdisk /mbr and the regular format c after that and did it twice to be safe.
Win 2000 decided that it was not going to be install. I installed XP Pro. I copied Win 2000 i386 file on the drive, formated c again and installed 2000 using the file on the d drive. Computer is up and running faster than ever. This is one of my friend's computer, he is now happy and he's telling everybody that i'm the best...... thanks guy