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I just finished building my Rostock Max V2 and when I reached the point in the assembly guide where it asks you to "Home" the printer. When that starts the x & z axis move up to the stops, and the y axis moves down. I checked the end stop switches and they are working (according to Repetier-Host all are :L to start and will switch to :H when pressed) I then switched in the configuration file "INVERT_Y_DIR" from "false" to "true" and when I attempted to home again the y tower sat there and ground a bit without moving.

At the suggest of another thread I found on here I switched the plug on the RAMBo for x and y motors. when I switched these both the x and y motors moved down and the z moved up (I had inverted the Y in configuration.h so I assume that is what happened). I then put the motors back in their respective locations and switched the first 2 leads on the y stepper motor, same deal.

I am not sure what would cause the Y motor to only go down, if it is something about how I assembled it, or if the motor is broken but nothing I have found on here has worked

The firmware I am using is 0.91

Most likely the stepper wiring is bad.
Could also be a bad RAMBO board, the easy way to test which is to swap over the stepper wiring on the board and see if the problem moves or stays on the same axis.
BEWARE You must remove all power to the board before disconnecting or connecting stepper motors, if you do not you can permanently damage the RAMBO board.

So I just switched the X and Y ports on the RAMBo controller and now the problem has moved to the X tower. Sooo it would appear that my rambo board has a bad y stepper motor terminal. Is this a fixable issue, or do I just need to get it replaced.

You can work around it, by using the second extruder output for the broken axis, it requires some messing around in the firmware.
But if you got it that way I'd contact support, they'll likely replace it, unless they have other ideas as to what's wrong.

I contacted support, so I guess I will find out on Monday what they think I should do. Just to be safe I ruled out the switches by switching the wiring for the x and y switches on the RAMBo to see if that moved the problem as well, and it did not.

Thanks for you help.

EDIT: I Changed the pinout that the code thinks is connected to Y to E1 (the empty extruder) nd plugged it in there so now the printer is working great.

2nd EDIT: The plug on the RAMBo for the extruder also doesn't work (Just sits there and jiggles) so I still can't print, oh well, I will have to wait for a replacement.

I am currently having the same exact problem with my rostock max v2. When I try to home my Y tower only goes down, regardless of changing the firmware as the manual instructs. Did you ever get this issue resolved?

Looks like you limit switch is engaged somehow - check connection to the board and continuity on the wires going to the limit switch. if all good then it might be your board