Can't use pop-ups or calls to web-sites via shortcuts, etc.

I'm not sure what's going on, but my pop-up blocker from IE rarely shows
itself and I dont' know how to get it to come up. I'm not sure that's the
problem or the result of the problem I have, however.
My best description is that when I am on a web-page, it seems that some
of the time the pop-ups show up and some of the time they are blocked. I
have a hunch, however, that it has something to do with Javascript, maybe, as
it seems only the popups that have to do with "action-able" popups dont'
work. they come up for a second, then they disappear.
Similarly (maybe), When I paste a shortcut to a web-site on my desktop,
some of them work while others exhibit the same behavior as the pop-ups.
Thirdly, when I am sent an e-mail that has a URL in it that I want to go
to, sometimes when I click on them, the web-site is called up, but sometimes,
as with the other issues, they seem to want to come up for a moment or two,
then disappear.
I don't think this is a virus, but rather some security setting, or
something wrong with Active Desktop or popups, or Java, or something.
If you go to the Jibjab web-site, there are two ways pop-ups are
called. One is the click on the recent musical things they have, which calls
the program up as sort a pop-up, while some of their older settings call the
software up in a different way. My computer will call up, then cancel the
first type of pop-up, but allow the second type.

Any help is much appreciated.

~~Rich