Sample: (Click for full size)

Note the rainbow lines (vertical in the scan, actually running across the film) in the image. These get closer together with higher resolution and farther apart with lower resolution. Setting it to grayscale only output looks just like this image desaturated; the lines are a bit less visible, but still there.
I've cleaned both sides of the bottom glass, and the exposed side of the top glass. Cleaned the scanning element with a camel hair brush and a puffer. I've used a pretty fair assortment of "streak-free" cleaners on the glass including Windex, eyeglass cleaner, methanol, and vinegar, with little to no change. This scan is using the glassless carrier, so no extra source of smudges there. I did try a fluid mount without the Epson carrier, and it still showed the lines, though a bit less visibly.
It's occurring with everything from Efke 25 to Ilford DP400 and Fujicolor 200, so it's not just one film having some sort of odd refractive effect.
As far as I can tell, the 4490 has no manual calibration process. The drivers are the most recent available from Epson's site, running on Vista Home Premium SP2.