crazymonkeyni,
I also have a Kossel Clear and recently made the switch to Repetier Firmware 0.92.4 from RC Marlin. Maybe I can help. It took me a little tweaking to get my effector moving, but right now I'm pretty close to getting this firmware up and running!
It sounds like you might have an endstop configuration error though.I don't want to post up my configuration.h file just yet, because even I don't fully understand how Repetier deals with delta endstops, but here is my Endstop configuration.
Endstop Configuration -
X Min - Not Installed
Y Min - Not Installed
Z Min - Normally Closed, Zmin pin
X Max - Normally Closed, Xmax pin
Y Max - Normally Closed, Ymax pin
Z Max - Normally Closed, Zmax pin
I do wish I better understood the endstops though. Maybe the admin can clarify...
The Kossel Clear has mechanical, normally closed endstops installed on the A, B and C towers at the top. It also has a identical normally closed endstop mounted to the effector, which acts as the "Z-probe". Here is the "pinout" of the endstops.
With this setup, what is the correct configuration for the endstops? Which end-stops are responsible for the X, Y and Z axes?