Where are you having a problem?
Is it the gerber layer and Excellon drill files generated by Kicad having a different origin point before they are loaded into Flatcam?
When you generate the gerbers & drill file with Kicad, make sure the check boxes for the origin are set the same for both, either absolute or auxiliary.
As a last resort if you load the gerbers and excellon files into the gEDa gerbv viewer you can apply an offset to a layer to align it properly and then save the layer with the new offset position.
I am using a nightly version of Kicad compiled from source but I think the origin options for the gerber generation were the same when I was using the stable version downloaded from the Ubuntu repository.
Version: (2017-10-06 revision d6c0d320d)-master, release build
Platform: Linux 4.10.0-35-generic x86_64, 64 bit, Little endian, wxGTK
wxWidgets: 3.0.2 (wchar_t,wx containers,compatible with 2.8) GTK+ 2.24
Compiler: GCC 6.3.0 with C++ ABI 1010