I have an aluminum I3, purchased in early November that is assembled and functioning. After some minor initial issues (bent rods, reversed steppers, noisy fan) I now have enough spare parts to practically build another one...all good from my perspective as the idea is to learn. I have successfully printed about 50 items ranging from calibration items to spool hubs and a few mechanical and robotics parts. So I understand the mechanics and the software. In general, the printer works....but it does not work consistently.
I have a Sanguinololu card with Marlin firmaware and am running Printrun. The software appears stable. Sanguinololu firmware is Marlin 1.0.0 as it originally cam from Geeetech.
Here's the problem. When trying to calibrate the filament flow rate, I am unable to get a consistent rate no matter what I do. I typically feed 100 mm of material and manually extrude 50mm as an initial test and then measure what is left, gradually reducing the measurements. Initially, the E-step was set very high for a Geeetech Mk8 extruder, so I reduced it significantly. But about every 3rd or 4th test the extruder feeds over 100 mm of filament no matter what I have the device set to feed and no matter what E-steps/MM is set to in the firmware. I can tell the firmware that e-steps is 10 and to spool 5 mm of material and it still prints out over 100mm. And about every 10th time, the extruder actually runs backwards!...and long enough to tell me it would be retracting a lot of material. There is absolutely no consistency to this issue at all. I'll get 2 or 3 good advances, then a bad one, then another bad one, then some good ones, etc. Temps are fine. No clicking.
A secondary problem that I can't track down is the occasional shifting of the Y-axis mid-print. Not a jam, loose wiring or a loose belt. I'll track that separately but thought I would mention it.
So, summary of issues:
1. Extruder does not operate consistently when calibrating. Manual feeds work fine once or twice, then randomly feeds out over 100 MM of material.
2. Extruder occasionally runs backwards when manually feeding.
3. These errors occur when attempting to calibrate (using manual feed option)
4. They appear to occur when printing also as I have several blobs of material that should be parts and a few parts that are missing whole sections whee there should be plastic.
So...what have I done to troubleshoot?
1. Checked all connections. No issues or loose wires.
2. Swapped pololu stepper card with another. Works fine.
3. Replaced the cable. No improvement.
4. Replaced the extruder stepper motor with a new one. No improvement.
I reviewed the entire Github Marlin Firmware issues log and do not see anything like this so I do not think a firmware update would help. There may be a few firmware variables that I'm not familiar with, but can't imagine that inconsistency like this is due to a single firmware setting. Has anyone else seen anything like it? If not, the only thing I can think of is a short, bad circuit board or a bad solder connection on the Sanguinolu card.
All suggestions welcome!

Thanks,
Scott