Extruder changes direction in middle of Print (no replies)

Hi this is a problem I have benn dealing with for more that 5 months.

My extruder changes direction in one of the machines, connected to a MAC OS, in the middle of print.
I am using Makerbot motherboard and stepper controllers,
I have another achine connected to Windows and this doesn;t happen.

I think it might me the software on mac, I a using replicatorG 040, with the latest Skeinforge.

I think is something on skeinforge

I am printing a lower carriage for a mendel now, and on 40 minutes the extruder changes direction of extrusion,
and then after 3 minutes it goes back to normal, correct direction of extrusion. The sae thing will happen at 1.20
minutes, so every 40 minutes. For another piece it changes de value, but still constant within the same piece.

Thanks to everyone!

I hope you can help me,

Rep Rap Argentina. José