Hi Geert,
according to my experience with calibrating exposures from old Canon 300D, the amp glow is only removed correctly when you turn dark optimization off. Then of course, your master dark has to match both exposure and temperature (again with 300D, +/-3C temperature difference seems ok). If you have more master darks with same exposure but different temperatures, I suggest to try to calibrate one frame with all those master darks and optimization off. Then, debayer and inspect the result to see which master dark yielded best result.
regards, Zbynek
BTW - idea for wide audience - wouldn't it be possible to separate dark current from amp glow using wavelets and optimize/correct them separately? For one-shot color cameras with bayer mask, one would have to separate channels (red, green and blue pixels separately) and then combine them again, but I think it's doable. I may experiment with this approach if I find a time for it.