Hey Tim,
stall homing works this way. That means, as soon as something blocks the carriage movement, the stepper driver “thinks” it has reached the home position (stall detect), thus the controller stops moving and sets the “homed” flag. There are roughly two reasons why an axis could block (besides bumping to the home position): Mechanical and electrical. You already mentioned one: Ball screw packed with wood dust, but you already excluded it.
Onefinity provides a help file which deals with many kinds of blocking of an axis:
I would check all points one by one to see why your carriage does not move anymore in the middle of the axis.
There are three causes that are not mentioned in the document above:
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Should your machine not be properly rectangular (“squared”), the Y movement can block.
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And the second possible cause not mentioned in the document above is: This mysterious issue some time ago.