CNC router occasionally makes jarring noise and home jumps when it does this. Help!!

[Washout]

There are way better guys on here than me to advise, but here goes....
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What you are describing sounds like a motor stall on the y-axis, which is likely due to 2 causes:
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1. You have a mechanical problem, such as the rails, ball or lead screw(s) or bearings being out of true and causing binding i.e. a resistance the stepper motor is having difficulty overcoming or;
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2. You have an electronics issue where data or pulses are getting lost and the steppers are not moving when they are supposed to be.
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For 1. I would see if you can first disengage the ballscrew/leadscrew and see if the gantry can be moved across its full range of travel with only a little pressure by hand - my own gantry weighs a fair amount but I can push it easily with a finger. Or failing that see if there is any adjustment possible on the ball/leadscrew alignment and redo that - not sure how your ballscrews/motors etc. are attached, so can't really advise on the method of doing this.
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For 2. Only advise I can give at this stage is if your wiring is not using shielded cable, then replace that with shielded CY cable and ground the shield at the control box end only and to the same ground point all the other earths on your machine should be going to, which should in turn be wired to mains earth. Make sure the ends of the shielding at the stepper motors are isolated i.e. not contacting anything. Other than that you are looking at driver, control board/BoB replacements, but I can't advise on diagnosing your existing components. Also I have seen some stories of inadequate grounding within the control box itself, so check that out.
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Oh also if the machine came with a cheapo parallel cable for connection to your PC then try another one. I had a problem with my machine getting spurious e-stops that turned out to be a shoddy parallel cable. Replaced it with a chunky shielded one and that problem went away.
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There'll likely be other guys that can advise further, but having tripped over most of the pitfalls in building reliability into my own machine that's where I would start.
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Hope that helps.