Java popup windows won't work

Java popup windows won't work anymore. I thought it was just because I'd had a virus about a year ago and maybe it was anti-virus stopping it. But some of them were coming through, or I'd get about:blank, or I'd get things like a calendar when trying to book flights and you click on it but it doesn't enter anything into the webpage. It's not urgent but it's very frustrating if you're on a page and it won't allow you to manually enter something, only through the popup window, because then I just can't use that page. I really don't think it's a security thing anymore because I just had a terrible virus on my computer that I got rid of with thanks to majorgeeks.com but it didn't fix that problem and it was still happening even when I turned the security levels to none to run some scans.

Anyway....any suggestions would be appreciated.
Thanks.

 

I had to reinstall java once to fix such a problem.