I'm just trying out my Raspberry Pi3 running Ubuntu Mate with INDI. Camera is ASI1600MM-C and all looks fine at that end. My client is a Windows 8.1 desktop running the latest Kstars/Ekos. No problem connecting tio the remote Indi and the cameras show up nicely. In the CCD panel I can capture successfully to Client although a bit slow to transfer the 32Mb file across the network.
Next step was to then try just saving the file to "Local" meaning the RPi in my home folder. That would eliminate the upload time and I save to a fast USB stick so its easy to then transfer the captures to my desktop for processing. Attached screen shot shows what happened. Instead of saving to /home/ken/Light Filter#1_001.fits, each letter of the file name has home/ken/prepended leading to the file being saved a million folders deep. Actually I think it is creating sub folders so instead of appending the subfolders it is appending each character of the sub folder names.
I then ran Ekos from within a Ubuntu VM and it behaves itself - see second attachment

Does /home/ken exist on the PI?

Yes it does.

Can you post a screenshot INDI Control Panel --> ATIK --> Options.. There should be a property that takes the directory and filename there

Well sod's law has come into play and today everything is working! I've attached the screenshots before, during and after anyway. I did look at the options yesterday and it was filled in with the long long path. I promise I was not dreaming it
I also had a look in the source code and thought that around line 90 of sequencejob.cpp the .replace could be the culprit. I was thinking some sort of 8/16 bit mismatch or memory leak perhaps causing a x00 or space in the additional path /Lights/Filter #1 to get replaced with the /home/ken root.
Anyway, if it happens again I'll post again.