For those of you with a Canon EOS M100 having the same issue, here is a work around. Jasem has been kind enough to remote in into my system and tried everything he could, tweaking the gphoto drivers etc... without success unfortunately.

However there is a work around that works well so far:

1) Set your mirror lock to the value of 10: The camera will lock up for 10s before the exposure starts
2) Set the capture format to NATIVE. This is very important. If you set it to FITS the camera sensor won't be illuminated and your picture will look like a dark frames... strange but that's the behaviour.
3) You can now exposures as long as you want without issues that fully illuminate the sensor

Note: updating the camera firmware has no effect... so don't waste your time here. You will now get CR2 pictures opening in the FITS viewer. Those won't be stretched properly and will look strange compared to pictures taken in FITS (at least for me...!). However they look identical to fits in other processing software like Astro Pixel Processor, Photoshop etc... so don't be alarmed... what I do is take a 180s exposure in FITS at 800 iso to make sure everything looks good (that exposure length doesn't not shutdown the camera when downloading) then proportionally adjust the ISO and longer exposure length and quickly import the first exposure into APP to double check.

Why bother with a M100 anyway...? well its really cheap on the second hand market, I got mine for $100, with astro modification it ended up cost me all up about $350 which is pretty great. It has the same ASP-C sensor found in the Canon D80, which is a new generation low noise sensor. It's very light compared to regular DSLRs. Downside? Does not support tethering natively, unless you use Ekos, Gphoto2 or Cascable which are 3rd party applications.

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