Several issues contribute to the mix here. (i.e. 1) the "B"/"M" dial setting problem with some Canon cameras like the 5D, 2) the FORCE BULB setting that can cause odd behaviour with these cameras and 3) the way Ekos handles shutter speeds that are not available in the user's camera). I'll try to explain them, maybe this will take another posting later tonight.
Niki, was your camera dial (Hauptwahlrad) set to "B" or "M" when taking flats? The problem with cameras like the 5D is you have to set the dial to "M" in order to have short shutter speeds timed correctly.
In addition, you have to make sure EVERY TIME that FORCE BULB is disabled. Unfortunately the state of the FORCE BULB option is not reliably saved. Occasionally it will be re-set to ON:
Example:
Set dial to "M", connect to camera, choose FORCE BULB = OFF, save Options. Shut down EKos.
Now set dial to "B", connect to camera, FORCE BULB can be ON (*), regardless of what has been saved. Once again choose FORCE BULB = OFF, save Options, shut down KStars.
Set dial to "M" again, connect to camera, FORCE BULB can be ON(*)! This may sound like it was not true but I swear I tested and re-tested it today numerous times. I can make a video just in case. All test were done with the latest and greatest nightlies.
One possible implication is this: If you set your dial to "M" (like for flat frames or short exposure subs of moon, planets, etc.) and FORCE BULB is enabled in Indi, all pictures taken now will be of the shutter speed that is selected in your "M" SUBmenu (Kamera Schulterdisplay rechts). In this case (dial="M", FORCE BULB=ON) Ekos can not choose any shutter speed whatsoever! If you're taking flat frames now, Ekos will DISPLAY all sorts of shutter speeds but IN FACT the pictures taken will all be of the same exposure time, i.e. the one you selected in your "M" submenu.
The third issue I ran into: If you manually choose a shutter speed (in Ekos) that is not available in your camera's "M" mode (like, for instance, 0.01s while the 5D only offers 1/90 and 1/125), Ekos will fall back to the "EOSremoterelease" method. What happens is Ekos will request a "B"-style" exposure from your camera but since your camera's dial is set to "M" the photo will be of the shutter speed that is currently selected in your "M" SUBmenu, too. I suspect none of these issues happen with cameras that do not have a separate "B" dial setting!
This is confusing to say the least, particularly for beginners.
(*) if it is not, just disconnect and re-connect the camera one more time and FORCE BULB will be enabled.