You can also plug in a mouse temporarily to your secondary PC, go to options in EQ, and change back to full screen, then back to windowed mode. The mouse wheel will start working again.
I'm not sure why this happens or why this is the fix, but its super annoying. I have to do it every time I play so I just keep a spare mouse around to do this. Seems to happen on my two oldest PCs that I use for my 5th and 6th boxes but not on newer PCs.