After a great deal of troubleshooting I pin pointed the cause of the errors being reported in the host software.
It began with continuing our electronics test of the extruder, I was getting the following error from the host software
ERROR: GCodeReaderAndWriter.getBTemp() - no value stored!
I came across this post and after running out of ideas I figured I try an earlier version of the host software. The electronics pasted all the tests using an older host software.
I purchased the electronics from ebay user raysyu who did not mention which host software version was used to test the electronics nor which firmware versions were used for the motherboard and extruder. After contacting raysyu I found that he tested the electronics using the 20100308 version of the host software which further supported the reason why our tests were failing using the newest host software version.