It seems there are a few issues with indi_gphoto since v3, Ive raised one here too: www.indilib.org/forum/ccds-dslrs/9317-cl...mk-ii-fits-file.html
Fits files arent being captured correctly for me on my 5D mkII.
I know this doesnt help your specific issue, although I hope we can get enough attention for it to be investigated by someone who might know the code.
Hang in there, fingers crossed it get resolved soon.