Flashcut can negotiate thru all sorts of mixed geometry be it short lines or short lines mixed with arcs without breaking a sweat when things are set correctly, so its not the control in itself....
Are you using, or have you done a "save as" for a new setup from your plasma setup file ? If so, you would need to scour thru it to make sure things set for productive plasma operation do not inhibit router operations
In your configuration/ feedrate/ramping section, is your Continuous Contouring Feedrate Tol. set higher than your start stop feedrate and ramping rate ? CCFT usually needs to be set higher or you can get momentary pauses at the end of geometry.
In the same place, did the plasma system have the Max arc feedrate (under General) set to a lower rate than your trying to achieve ?
In your configuration/ Motion Delays, has there been a change by chance to the "Direction Change Delays" or "Corner Delays" ? ?
Flashcut does not have a specific setting for anything like "exact Stop" others are familiar with.... so it can't be that.
I'll give this some more thought as to what you might be seeing there.......