After replacing hard drive, and installing 7 again, first thing I did was install super antispyware and malwarebytes and ran scans. Had 43 infections just from start up on new hard drive.
That sounds horrible... Do you have other storage media connected to your computer while you're doing your install? USB flash drive, external HDD, internal backup drive, networked? Sounds like something is migrating to your new partition after install...
I've never experienced any infections during a windows setup from XP forward even if connected to net during install, but something is buggering you up... try this maybe:
have super antispyware and malwarebytes burned to a cd
disconnect all media but the partition you want to install to - USB flash drives, externals, etc
disconnect from any networks
go offline for install
install 7
install antispyware and malwarebytes
run scans on both (if any is discovered there is something bigger going on)
connect online and install MSE (let it update and do its initial scan)
begin your windows update path
now scan media (USB, external, etc) to figure out where your infections were coming from.