Flashforge/Powerspec 3D Pro - Replicatorg producing bad quality prints intermittently

[lolwut]

So, here is a little backstory. I purchased this printer a few months ago, I started using the makerware software with great prints (only issues were warping -- even when using hairspray on glass and 85-90 degree bed temps) and then felt comfortable to dive into the replicatorg settings. I believe my extruder heads are mk10 (Teflon tube inside the heads) and have the shorter nozzles.

I tweaked a few replicatorg settings and my prints started to come out better than my makerware prints. I solely started using replicatorg and most recently I have started running into issues. Here are the pictures of a test print:







I tried a more expensive brand of filament and the same issue occurs.

Its important to note that the filament is the same, the stl files are the same, but the replicatorg prints are aweful and the makerware settings at 15% infill and .20 layer height (same bed level, same extruder) come out awesome. I've paid attention to the gcode and for some reason it will print great on the first generation of the gcode > .x3g in replicatorg, but then it will turn to crap over the next few projects.

I haven't tried printing anything else to see if it may be the file. I did notice this morning before I left for work that my bed is a slight hair off level on the right side (I'm using the right extruder for these prints) but I use the same extruder with makerware...and...replicatorg!

Again with makerware my settings are: (always print from sd cards)

printer = replicator dual
infill = .15
layer height = .20
extruder heat = 225
bed heat = 85
speed/travel = 40/50

Again with replicatorg my settings are:

printer = replicator dual
infill = .15
layer height = .21
extruder heat = 220
bed heat = 85
retraction speed = 20.0
feed speed rate = 40
feed flow rate = 40
first layer feed rate = .9
speed travel = 55

Should I uninstall and reinstall replicatorg?

Any help would be appreciated!