I agree, it would be good to know why it is throwing errors (what does the 44061 even mean?), but with one day left until ship, I'm sure that a rookie team just wants to bag a functioning robot.
My team, LASA Robotics, was encountering this same issue. We lengthened the safety timeout to 3 sec. and all our errors went away.
On the original issue, if you are using the KOP ribbon, you should read this:
http://www.usfirst.org/sites/default...structions.pdf
that would explain the mismatch of channels in software and hardware.