Internet Exploreer closes new windows

I have recently reinstalled Windows 98SE on a computer I just overhauled that had more problems than you can shake a stick at, not booting right, not shutting down ect. Everything went fine except that the IE 5.5 and 6 as well as Netscape close every new window that you load up. It is not related to Anti Virus, and it is not related to anti pop up software. I also tried to close the Java settings, which worked for a few days and now it has started up closing explorer windows again. Please help.