"Does this mean that drawing a selection to this test stack isn't slow?"
Yes, on the test stack, it is fast
"Did you save it as a TIFF-stack?" - went to Save As-> Tiff. So I am assuming this is a Tiff Stack
Yes, the extracted rectangle is saved as a tiff with 2 channels
see this: I then split the original file/extracted rectangle stack by Image>stacks>Stack to Image. If I try to draw ROI on one of the split images, it is still slow; however, if I SAVE the split images, close the split images, the reopen the 1 split image, it is fast!
So, I am wondering if it is setting some settings that aren't modified even when image is split.. They only change when it is "refreshed" (ie, split images closed and reopened)