Filawinder: near-dead motor or software bug?

Hello everyone,
I've been working on operating the filawinder now for about a month or so. Since its' assembly was completed, I've encountered two issues, 1 minor and more recently 1 major:

Minor issue is that the guide arm is seems to be completely non-functional. It has never moved other than by my hand, not even for a malfunction movement. I have reset its' setting numerous times, by the filawinder manual's methods, to no avail. Magnet for the Hall sensor has been North-facing-out checked and re-installed 3 times now. Checked wiring numerous times as well. Been beginning to wonder if it may just be a bad servo motor.
Therefore... I modified the winder's physical setup to extend the distance between the winding spool and the PTFE guide loop exit from appx 6inches and lengthened it out to appx 32 inches.
Also, in manual mode, the motor doesnt turn at all and the potentiometer doesnt change it 'not moving' either.
Since that change, it wound up a kilo spool with no problem regarding filament binding or winding up on one side.
Minor problem negated by changing the engineering of how the filament is guided onto the spool.

But the more recent, and definitely more major problem encountered is the photocell system seems to be malfunctioning.
I can hear the winder motor trying to rotate when the uppermost photocell(1) is blocked, and its tries to uptick the winding rate as photocell's 2 and then 3 are blocked, but the moment the filament's shadow even touches the bottom-most photocell(4), the motor stops rotating, and the laser flips off for about .75-1 second, then the laser turns back on. Also when the laser flips back on, a white LED on the Arduino board flips on as well.
Already have tried to recalibrate it(about 15 times), tried recalibrating it with the outside light shroud on and off, even tried recalibrating with the room's ceiling light off.
So at this moment, this winder is non-functioning. Seeking a mini-usb connection to check the software and a volt-meter to check the potentiometer... Pretty sure there isnt a 'reset to factory' button on the board itself but ill check into that later tonite.

Further description of the problem:When in manual mode, the motor flips on slow for like 0.1 second, but then motor turns off, and the same white LED blinks on the board, then it waits about 2 seconds, repeats. It'll take like 1 hour for it to rotate about 3 inches on the spool side of things.
When i go to calibrate, the laser stays on, but once the calibration window has passed, and it reverts to manual, it just falls into this pattern. Furthermore the laser turns off when the motor stops.

Is it possible that the winding arm's malfunction or the potentiometer's malfunction is affecting the software's actions in regards to the winding motor?

Any insights into this malfunction will be greatly appreciated

Thank you
AmoebicApplications