Some perimeters are fatter than others (Problem in Slic3r but not Cura)

[FailFTW]

I am trying to iron out some bugs with Slic3r that are either insignificant or not present in Cura. Basically certain perimeters may get fatter or smaller and will appear as bands around certain parts of the print.
I have some pictures describing the problem:

20160113_223550.jpg20160113_223834.jpg20160113_223917.jpg20160113_224009.jpg

The boat with all the pencil marks is in Slic3r, the other is in Cura. I cannot make out any warping or drooping during the printing.I have done 6 of these with Slic3r and 3 with Cura and have solved many problems along the way, but I cannot pinpoint what is causing issues here.

I have experimented with printing the Inner vs Outer perimeter first, and with placement of the seams. Doing inner perimeters first + random seam placement helped in certain areas like the bow, but had little effect elsewhere. On top of that, many of these bands end up in the same locations on the print with different settings.

Any idea what might be causing this?

Edit: In earlier prints before I took care of the seams, the seams where the perimeters started got too much extrusion as shown in the following picture:

20160114_000855.jpg

My setup is:
- FF Creator Pro w/ Sailfish 7.7
- Sainsmart White 1.75 mm PLA
- Klapton Tapeed Bed
- Slic3r 1.2.9 and Cura 15.04.3

Settings are nearly identical for both slicers:

- Extruder: 200C first layer, 190C all others
- Bed: 60C first layer, off all others
- Cooling Fan: off first layer, fully on at 3rd layer

- 20 mm/s 1st layer
- 40 mm/s infill and inner perimeters
- 60 mm/s bridges
- 20 mm/s all others

- 0.3 mm height first layer
- 0.2 mm height other layers
- 0.8 mm width first layer
- 0.4 mm width other layers

- 15% Rectilinear Infill
- 2 perimeters
- Printing order: Inner Perimeters > Outer Perimeters > Infill
- 3 Top/Bottom solid layers