Something I’ve never seen before. My CO2 laser fires at a higher output at the start of the cut for at least a good second atleast.
I can see this happening as the purple light in the tube, which gets noticeably brighter at the start of the cut, and the material is cutting, actually making a sound as it’s cutting at this point. Does anyone have any ideas?
Opinion: the high voltage power supply is failing.
The supply regulates the current through the tube, which is more difficult immediately after the tube fires because the supply must reduce the output voltage as the current abruptly rises. A good supply gets control within milliseconds, which is why nobody notices it.
If the machine has a tube current meter, you’ll (probably) see an abnormally high value in that second while the supply wakes up and gets control.
Replacing the supply is the only practical way to confirm or refute that diagnosis. Buy from a seller specializing in such things, as the folks who also offer beachware and skin care products tend to have sketchy hardware. Make sure it has the proper high voltage connector on the anode wire.
Assuming you get an identical power supply, installing it requires little more than unplugging the connectors, unscrewing the old supply, screwing in the new one, and plugging the connectors.
rather anoyingly…..Just installed a new supply, and the issue persists.
Id have a current meter that I’ll be installing.
Make sure you have good instructions for the installation. Do it wrong and you have 25KV on the meter.
Verify: one careful measurement outweighs a thousand opinions. 
On the upside, you now have a backup supply.
A second is much longer than delays in the layer timings. AFAICT, the only event that long is the exhaust air fan control, which simply prevents the job from starting while the fan spins up.
The power supply has only two inputs from the controller:
For a long slow cut, the tube power will be lower at the start if the speed is below the controller’s Start Speed, which is typically 10 to 15 mm/s. That won’t produce higher power at the start.
Assuming you have an “ordinary” laser under about 200 W, the cathode lead will be an “ordinary” wire with normal insulation, not the thick high-voltage insulation on the anode wire. Make solid connections: if a wire falls off a terminal, the HV supply will force an arc across that thin cathode insulation and wreck something.
We had an instance where a 500 W (!) laser had a split power supply with high voltage on both the anode and cathode leads, which produced a spectacular failure by arcing through the milliammeter. If the cathode lead on your laser isn’t an “ordinary” wire, don’t install the meter!