Bizarre printer operation... help?

A video would certainly help

It kinda sounds like a problem with the drivers for the steppers....or a communication problem with the computer??? what's the background on the setup? printrboard? windows? etc...

Ah, I forgot that important background:

It's a Solidoodle 2 with the original sanguinololu electronics. I haven't modified them in any way.

I'm running Windows 7 and normally connecting with Repetier, although I also tried pronterface in my troubleshooting attempts.

The movement is accurate to what the control software is expecting, except when I get the loud buzz followed by some small amount of choppy motion. So it really does seem like a communication problem, but I've done everything I can think of from the USB cable back to troubleshoot and gotten nothing. Could something have gone bad on the board, while just sitting around powered down, to cause a communication problem like this?

The drivers shouldn't be overheating, they each have a heatsink and there's a 50mm fan blowing on them. It shouldn't be a problem with heatsink adhesion either, those have been on for about a month now, and I used thermal epoxy to attach them so they can't have shifted or come loose.

One more (possibly) related detail, although I don't know how this could be causing it... The new extruder motor seems to be wired backwards.

I wired it exactly the same way as the stock motor, but apparently color coded leads don't mean what I assumed they meant. Hitting extrude makes the motor run in reverse, and hitting retract makes it run forward. I figured I'd get around to fixing that when I got the bowden setup working correctly, but never got that far.

I don't think this could be related, though, because everything was working normally for at least an hour with the extruder motor wired backwards. But hey... this is so weird I figured I'd throw in all the details in case I'm missing something simple.

I haven't actually tested the motion with the bed or extruder on, all of this (videos included) is done with a cold bed and extruder. I haven't unscrewed, removed, and reattached the power connection but I did check it and it sure SEEMS to be in there as solidly as ever.

I had seen that too, this same choppy movement (without the high pitched noise and failure to move) when homing before starting a print and then the print is normal. Unfortunately, the current choppiness persists whether I'm manually moving things or it's running a print.

I've experienced this choppy movement before, but only if I have "Show filament" checked in Repetier.  Turn it off if it is on, as it takes up processor cycles.  Works fine with it off.  Running Win 7, 64 bit, with 8 gigs of ram, but still happens when I watch it draw on screen while printing,

The voltage shows as 12.7 volts at the screw terminals, and at both of the easy access 12v points I know of on the board. The supply seems to be ok.

After further playing, my earlier impressions were wrong. The speed the move is done at makes no difference to whether or not it's choppy.

However, I've discovered that the beats (or pauses, if you prefer) are regular like ronsii mentioned. They're not regular with distance traveled, though, they're regular in time.

No matter what speed you move at, the beats occur every 1/4 second (or as near as I can figure by tapping my toe to the beat and comparing against the second hand of a clock). So why would it be pausing in a pattern of 240hz (edit: my stupid mistake, it's pausing at 4hz or 240bpm)? Has the microcontroller been damaged?

While I was working on getting the new extruder attached I completely removed my electronics cover and, in the process, left all of the screws holding the board in place out. The double sided tape connection under the screw terminals seemed to hold it just fine. However, what I noticed (after applying power to the board, unfortunately) was that there are metal spacers under the board which aren't actually connected to the case as I had assumed. So... all three of them fell out, and in the process one wedged against the top two programming terminals on the board (the ones labeled 5v and Ground).

I immediately pulled power, saw no magic smoke escaping, and figured it was ok because on power-on the board responded and everything seemed ok. But now I'm wondering if the problem didn't begin then and I just didn't notice it for an hour or so because I was futzing with the extruder and not gantry motion (and the only thing I did to confirm that the board was still controlling things was homing the axes when they were already at home, meaning a short less than 1/4 second move).

I'm thinking I'll try reflashing the firmware and see if that works/fixes anything. But if that fails, or fails to resolve the problem, maybe I'll pop a new controller in. Luckily, I have an extra Atmega1284P with a bootloader and vanilla Marlin on it that I can try instead. Here goes nothing...

Did you say you have not put the metal spacers back in (the ones between the board and the case)?  If not, put them in.  I have had weird actions while working on the board with it powered on.  I think it is some strange grounding thing.  With the spacers out, crazy stuff, with the spacers in, everything fine.