I'm telling ya... jack your feed rate back up to where it was originally, manually stick a G61 in a line by itself right before the tool first plunges into the work, and put a G64 at the end of it all and it's going to fix your problem. If you're not running a Fanuc control, I'm sure other controls have the same Exact Stop Check Mode functionality, although it may be called something different. You'll just have to find out how to call it up.
I just noticed my Mori book calls this - Function For Accurately Positioning At The End Of Linear Movement. If that doesn't ring a bell for you I don't know what will.
G61 (Exact Stop Check Modal Command)
G64 (Return to Normal Cutting Mode)
G9 (Single Block Exact Stop Check) Works only on the line that it leads.
What Exact Stop check does, is it forces the the machine to wait until all the servo errors and lag have resolved before moving onto the next block. I can see in your part where you're starting and ending cutting, and you're right it's coming up short. Exact Stock Check will fix this.
I have a job where I create a 1/4" closed end slot which I come back to with a DA cutter to chamfer. The chamfer is big enough to do both sides at once, so I'm running in a straight line down the center of the slot at a high-ish feed rate. Without Exact Stop Check, you can see that the chamfer on the end radii of the slot is less then the one at the beginning. Same thing that's happening to you. I turn on Exact Stop and the chamfer is even on both ends.
I have another job in UHMW that is nothing more then three square 1/2" wide 1/4" deep slots spaced 1/2" from each other and each square path being one inch bigger then the previous one. These slots also have rounded inside corners so it's not a perfectly square tool path, but almost. There is a male and female version of this part that have to fit closely together. I run the job without Exact Stop Check and they will not fit together at all. Using the very same tool path and turning on Exact Stop Check they'll fit together perfectly. It's simply the nature of the beast. That being a servo driven machine tool.
This phenomenon of machine tools is spelled out in all the control manuals with vector traces and charts and you name it. Most of the time it doesn't matter, but I'm sure many around here have similar war stories as I do about needing to deal with this minor shortcoming. Thankfully the control manufacturers have supplied options to deal with it. There's also things like Look Ahead and my favorite mouth full... Quadrant Projection Compensation Function. But that's for another day.
Dave