Feed per rev G95 way too fast

Hi, Sorry, please bear with me, I'm new here and relatively new to LinuxCNC.I've been converting an old Boxford 240 TCL to LinuxCNC running on a Pi5. 

Everything is running fine(ish) there are still some glitches and errors that crop up and the odd latency warning too (stepping is done on an EC300 running remora so I'm not so worried about the latency warning).

However... i've gotten to the point of testing, and for some reason in G95 and feeding at 0.1mm/rev the axis runs at way faster rate, 10x maybe more.Anyone have any idea what is going on?  The only other thing to note is that I am having issues with LinuxCNC seeing my index pulse, but it is seeing the count from the single encoder (100 slot disk with a second slotted opto switch for index so not quadrature). 
I'm assuming that its possible the feed issue could be linked to that.

The other issue I am having is when i run a program, it won't run through automatically.  The only way it will run is by me hitting the single step through button.  I'm wondering if that is linked to the encoder also as perhaps LinuxCNC isn't seeing "at speed" so isn't letting the program run?

hal and ini attached.  Please forgive the messy files, once they are running right I'm planning on cleaning them up.