What continues to puzzle me is that disabling the CHDK overrides seems to eliminate the problem, at least for the shutter speed/aperture/ISO settings that I can duplicate with the normal Canon options.
Normally, the Canon firmware takes a dark frame if the exposure is longer than a certain value. The exact value varies by model and settings, but is often around 3 seconds. If a dark frame is taken, you should see "BUSY" after shooting, for the same length of time as the exposure. Amp glow should be minimal if the camera does a dark frame.
If you turn off dark frame in CHDK settings, then you won't see the BUSY and your image will have more amp glow and hot pixels.
It's possible that when you use CHDK overrides, the normal dark frame logic isn't triggered. For example, if you set shutter to 15s in the Canon UI, you get 15s of BUSY, but if you set 15s using CHDK overrides, you don't. In that case, you could try forcing dark frame on in CHDK settings. If you still don't get BUSY for the exposure time, it could be a bug in the port.
Note you may see BUSY briefly for other reasons, like noise reduction at high ISO, but it should if it's doing a dark frame for long exposures, because it will be equal to the exposure time.