UncleSpam: Have you tried turning it off and on again ;-)? Really, some monitors don't always sync on the first try. Also, a "reflash all" may help if something in the flash got corrupted (sometimes happens on computers with bad PSUs and old caps).
Demolition, d0pefish: I am trying to make sense of that bug report, but currently cannot think of a place where this is happening on the digital side within Indivision AGA MK2.
If it would be happening in the pixel multiplexer (located in my memory controller), colour shifting would happen all the time for all pixels. That would be the first place I'd look for the cause, because I have tweaked quite a lot on the SD-Ram controller lately in order to fix flickering pixels and the vertical lines that happened "every 341 pixels".
This *may* be related to the double-datarate interface to the DVI encoder chip, which is also the DA-converter. Is this happening on all output pixel clocks? If not, what output pixel clock are you using for the mode where the colour shift is happening?