I've been playing around with it, fixing up the aspect ratios of the images. Now that I've got the hang of how it works I can certainly make some changes.
First, the logos are too large (they appeared smaller in the editor I was using and I only noticed how big they were when I checked out the portal page). There is definitely an opportunity to adjust the size that way.
Second, I'll take a lot at what the tallest logo is and make sure that none of the stacked pairs (one on top of another) are taller than the tallest vertical one. It might make the loop longer, but since we are scrolling horizontally that does not take up any extra real-estate.
Third, I'm thinking of slowing it down a bit. That might help with the CPU usage.
Lastly, the scrolling affiliates logos are only on the portal page. They are not on the main forum pages. While I was playing around with the options they did appear, briefly, on the forum pages as well, but they are now back only on the portal page (the portal page is the one you see when you go to gmhockey.com, and when you click on the portal icon next to the Home icon (the little 'P', but that icon may change as well).
I almost never go to the portal once I'm in the forum. I just use the "Latest topics" to navigate between the active discussions.