I'm not sure about coding in IE, all I know is that when I switched from IE 5 to 6, popups are much slower.
As for popups, I can see your point with there being some need for them. However, I still believe navigation is much better without them.
For example, I click on the thumbnail, it make picture bigger, I click on that, and it loads popup of picture. Then user has to find popup window, look at pic close it, then go to other window to click on more links to go back to index thumbnails.
I think that if header info above big picture is shrunken or eliminated, this would pretty much eliminate need for popups. For example, you click on thumbnail, takes to bigger image with forward and back arrows above/below pic, then you click again and it loads big picture on same page with no back/forward arrows or other text on page.
Then this pic could be hyperlinked with javascript history code to go back one or two pages when you click on it.
It looks like you already have this code in place for popup. It just has be made where it loads on same page.
Just my opinion. So far Coppermine seems to be best free picture program I've seen.
How can I edit maximum size for picture?