At this point you might want to just unplug and wait to hear from Support. Sorry. 
Yup, that’s what I did. Like i said, it’s getting worse.
Since it does the fast travel at the beginning correctly, it makes it harder for me to speculate. Since you’ve eliminated gunk on the rails or v-wheels, my guess is an almost loose set screw (though I’d expect that to be a problem on the fast travel) or a developing break in one of the wires connecting the right Y stepper motor. I’m guessing that’ll need a warranty replacement
Ouch!
Part of my day job includes designing gantry motion systems like the one used in the glowforge. There are a bunch of things that can be causing this issue, saddly none of these are user serviceable.
In order of ascending cost:
Stripped drive belt teeth - If the teeth on the drive belt become damaged the X axis cross beam stop moving when the missing teeth get to the drive cog connect to the stepper motor
Loose drive belt cog - The cog that drives the belt can become loose on the stepper motor drive shaft. Even though the stepper motor is doing its job correctly, the force isn’t being transmitted to the belt because the cog is just free spinning. This is most common on set screw style cogs. Clamping, keyed, and splined cogs are less likely to have this issue.
Bad electrical connection to stepper - If there is a loose connection between the stepper motor and drive electronics the stepper will stop doing its job correctly. Either it isn’t getting adequate power or it’s not getting the command signals to move.
Damaged Stepper Motor- Stepper motors spin back and forth, and that can lead to fatigue failure of the shaft or failure of the bearings if there was an undetectable defect in one of those parts.
Damaged Driver Electronics - The electronics that send power and command signals to the stepper motor can fry. These electronics are sometimes on a separate sub-board and sometimes on the main mother board. The cost of fix it is determined by what type of board configuration it is.
Luckily you should still be under warranty.
May your new unit arrive quickly!
Like watching a horror film.
Oh no! Thanks for letting us know about this, and i’m so sorry for the trouble. We’re looking into it now. I’ll update this thread when I have more information.
Upon investigation, it looks like your unit has an issue that can’t be resolved remotely. I want you to have a reliable unit, so I’m recommending we replace this one. I’ll be in touch via email to sort out the details.
I’m so sorry for the bad news.