I do monuments, and I know full well the issue you're having.
So here are a couple of thoughts:
Blade -
I know it may seem obvious, but make sure you are using a sharp blade. Any letter that features acute inside angles is highly susceptible to the problem you describe. But beyond that, check for:
Backlash in the theta axis -
1) Remove the dial head cover and check to see if the theta belt is missing any teeth. Missing teeth may cause a lag in response time needed to turn the knife when going into the next cut
2) Check to see that the gear attached to the theta shaft is not loose. A loose gear may cause similar effects as #1.
Backlash in the X or Y axis -
3) While the machine is in standby mode, gently apply pressure against both sides of the cutter head to see if it moves. Also, gently try to roll the drum back and forth to see if it moves. If so, you 'll need to adjust accordingly per the instruction manual.
Knife Elevation -
4) Carefully watch the knife as it lowers into the material, and then rises at the end of every cut. Is it dragging across the material? If so, adjust the wear shoe (of lift fork) that rides on the cam bar.
I can't say just why your plotter cuts fine in one case, but not another but I highly suspect some sort of backlash (sloppiness between gears, or sprocket and belt), coupled with knife elevation is to blame.
JB