Windows 7 corrupt disk problem?!?

i used an acronis bootable flash drive to help partition and set up my windows 7 partition and when i did this without realizing (please tell me if this is even a problem) i made the partition logical instead of primary and it is not set as active. this partition is about 30gb along with an 80gb vista partition that what originally taking up the entire hdd. after the first 2 times of booting up, live mesh beta and media center made popup notifications saying the disk is corrupted. when they do this firefox also acts up by opening an untitled page instead of my homepage and it wont successfully load any pages. it looks as if they are done loading but the little icon never stops spinning. i had what i thought was a permanent fix when i booted back up into vista and did a chkdsk with acronis on the 7 partition and it worked once. i dont want to have to do that everytime so any ideas? is it not worth the trouble and i should just do a reinstall? thanks

ps. i also had a problem where in 7 the window color would change from whatever i had it set, to a custom color (which happened to be black) everytime i opened up explorer. no matter how many times i changed it back it would just reset when i opened explorer, not really a big deal but i was like what the hell?

thanks for anyone's help and sorry for the long post!