Vertical band - G-code problem?

I'm trying to run calibration prints on my newly built Mendel90 and whilst things are improving there is a long way to go. One of the issues I have noticed on the .5 mm thinwall cube print is that I am getting a vertical band/blob on the corner of the perimeter where the machine starts printing, coupled with (it seems to me) a lack of plastic in the next few mm. (as in the attached photo - printhead moving counter clockwise). This happens regardless of speed/head/bed temp or cooling (this is fortunately not my best print yet just the clearest one of this fault!)
I've looked at the G-code produced by Slic3r and I wonder if the problem is here....

G1 X88.915 Y110.280 E3.21136
G1 X88.913 Y107.098 E3.27640
G1 F900.000 E1.77640
G92 E0
G1 Z0.420 F9000.000
G1 X88.855 Y107.032
G1 F900.000 E1.50000
G1 X88.849 Y90.415 F3300.000 E1.83971
G1 X88.980 Y89.536 E1.85788
G1 X89.200 Y89.215 E1.86584

At each layer change the code finishes an X/Y move with extrusion, it then seems to do an retract without move (3rd line) before resetting the the Z move and then an XY move at the new height without extrusion? Do I need to do a bigger retract, but also I seem to be missing the re-extrusion after the retract? Can anyone tell me if this is normal or what my problem is? [This is PLA btw]

Mendel 90
Sanguinolulu
MkII heated bed
J-Head MkIV B
Marlin
Pronterface
Slic3r 0.7.2B

Is the filament slipping? when the Z lifts, maybe since the filament isn't flowing, something gets too cold/hot in the nozzle and starts to stick. Do you use a fan on the nozzle? are you sure the temperature is right?

Set the nozzle to temp then move all the way up and down and see if the temperature changes. Maybe the current draw is taking something from the nozzle.

When I have flow problems 99% of the time they are down to the filament slipping on the hobbed bolt.

I've tried this at different temperatures so I'm fairly certain temperature isn't an issue. I did consider filament slippage but it would be unlikely I'd only be getting it at the Z moves, and the G code still appears strange to me (even if it's right I'd like someone to explain to me why it is as it is)

I've seen strange, unnecessary moves at times from the gcode created by slic3r.. try creating the same model just a tad bigger or smaller and see if it jogs the algorithm away from the problem point.

Another thing that mucks up extrusion sometimes is too much retraction. I have mine turned off completely and the temp low as possible and it works better for me that way.

Also, it looks like you're printing a tad hot.

You're probably printing too fast and not allowing the previous layer to cool down a bit before laying down the next layer. Turn on the cool option and set it to slow down so that the minimum time for each layer is around 20-40 s.

Thanks for the suggestions guys I'll hopefully give them a try this evening