I'm having the same problem except I'm using FeatureCAM and it is both starting from the beginning regardless of where I "set next line" and "run from here". It then slowly cycles line by line to the line where I had specified the "Run From Here" to be. Additionally, my toolpath is extremely slow to generate. This particular program is a 3D machining toolpath with approx. 22k lines of code. The post processor is configured to define 1 digit code numbering increments. When initially loading the problem I'm hanging on just the 19th line in a G54 command.
I suspect the "Set Next Line" and my initial loading issues are related. Has anybody made any headway on this?