With different filaments, even from the same manufacturer, may have different diameters.
I;ve had Makerbot PLA (Purple and Red) spools where the Purple was 1.80 and the Red was 1.76. If you have your Slic3r profile at say 3.0 (as mine was in the beginning for some reason), and you load filament at 1.78, then the extruder is expecting more than what is being fed causing wall and infill issues.
I would say to triple check the extrusion multiplier, re-calibrate the extruder, check your filament's diameter ANYTIME loading a new spool (in a few spots to check consistency), and then if all else fails, dial in your VREF if you have not.
Printit Mason and Printit Horizon printers
Multiple SD2s- Bulldog XL, E3D v5/v6/Lite6, Volcano, Hobb Goblin, Titan, .9 motor, Lawsy carriages, direct Y drive, fishing line...the list goes on
Filawinder and Filastruder #1870.....worth every penny!