Sorry it came across like that. Not picking on you.

For the record The FFCP works best with either S3D or Makerware. Flashprint is not the preferred option. FP was initially brought out with the Dreamer as an attempt at a Stratasys/3D Systems-like setup. Not too popular if I recall.

The USB issue goes far deeper. In a nutshell using USB for printing is asking for trouble. Stick to memory card or wifi.

If you had no clicking then your filament idler wasn't exerting enough pressure the the extruder gear. Easily remedied. And may be the case here although its unlikely.

Missed that part about both extruders. Whatever the OP tries to fix the issue he should try on both extruder to make sure it replicates.