I've had issues in the past with my drive gear "eating" my filament. It seemed that the filament quit extruding for one reason or another and the drive gear would slowly eat away at the side of the filament.
I eventually assumed it was the plastic filament guides causing unnecessary tension that the drive gear couldn't compete with, ultimately keeping the filament from moving forward. Thusly, allowing the drive gear to continue "trying".
My solution was to hang my spools above the machine to avoid using the filament guides feeding from the back of the machine up through the top.
Can the plastic filament guides really cause that much drag? What other variables can I expect to look out for?
Machine: MakerBot Replicator Dual (1st Generation)
The friction inside of the guide tubes is fairly minimal assuming that the lines are straight and there isn't anything else inside them. My guess would be that you may have another issue. Reducing the drag in the guide tubes while it may reduce the problem of clogged nozzle, might just be hiding the symptoms of another problem.
I've heard, but never tried adding a dab of Canola oil to the tip of your filament prior to feeding it into your extruder. Specifically for Makerbots.