When I schedule a job taking multiple photos and storing the pictures on camera, I end up with 2 versions of each photo on the memory card. The first is with an exposure of exactly 1 sec. and the second is with the exposure I initially set, for example 60 sec. That way if I want to have for example 100x60 sec. exposures, I end up with 100 photos of 60 sec. + 100 photos of 1 sec. That happens only to photos stored in the Canon’s memory card. If I chose to store the pictures on the RPi, or on the local computer I have only the photos with the exposures I set. Am guess I’m missing something in the Camera settings, but I can’t find it. Thanks if you can point me to the right direction.

This sounds like you have mirror lockup set on one thing but not the other. If you plan to do mirror lock up you need it set in the INDI control panel and on the DSLR. I had similar problems when I was using my Canon DSLR.

My guess why when you're only saving to the PI is that INDI is thinking that it is doing the mirror lockup and doesn't want to read the 1sec image. But when saving to the camera card the camera knows that it just did a 1sec and then a 60 sec exposure.

Also I might add that if you have the 60 sec images you could look at the for the quality to see if you're getting mirror shake issues. Effects of mirror shake are subsec so a 60 sec exposure should compensate for that. It will be a personal choice but you're effectively been taking 60 sec exposures without mirror lockup so there may be no harm it turning off the mirror lockup within Ekos.