Sounds like you were using 1/8 microstepping and whatever went bad caused you to go down to 1:1 stepping. Check your stepper driver, there might be jumpers to set the microstepping mode, and check any cable connection between your mb and your driver
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Also try swapping your x and y drivers and see if that swaps the problem axis... Will tell you whether it's the driver or the mb that went bad
Now that you mention it, I recall a few threads on the old makerbot group to that effect... Might've even had it happen to my first driver, replaced by mbi for free..