Ok well you don't look over tuned. 1800mm/min velocity isn't overly fast but it could be at the upper limit of tight or worn machine, esp these low power machines with crappy electrics. For a test you could drop velocity to 1000mm/min.
Personally don't think this is the problem has the code use's very few G0 rapid moves, plus most are Z axis moves and the G1 commanded moves are all low feed moves.

The G-code is fine and everything lines up. I've Attached combined files. Combined_Tracks_Plus_Drills.txt.zip

First for simplicity's sake I would check the mechanics of the machine.
Check for loose couplers or signs of slippage.
Check ballscrews for end float and ballnuts for backlash.
Check all axis for binding screws or linear bearings things like this can easily rob steps from a low power machine.

One problem I've encountered with these machines is very poor quality wires and connectors, esp the stepper wires. Infact the whole electrics are shit.!!
Go over the wires and connections with fine tooth comb. To be honest For the price of few meters of shielded cable it's worth replacing the stepper cables anyway. Electrical noise could be affecting the motors and shielded cable grounded at the controller end only will help reduce this.

If the electrics check out ok and there's no binding etc in the mechanics then can't suggest anything else other than trying on a different PC in case you have parallel port issue.?

After this if your happy with the machine and it's mechanics(so long has it use's ballscrews not lead screw) then I'd throw away the crappy all-in-one drive boards and put some decent motors with 50v drives on it along with 45V PSU.
This will sort any electrics problems and make the machine fly.

Good luck.!