I have decided to migrate over from Simplify3D to PrusaSlicer, simply because S3D's update is now delayed to the point where many are asking if it will ever be released, and the free slicers are getting to the point where they are better, with improved features etc.
Ever since the switch, I was getting bulges at the start and end of each layer (this happens on all of my printers, all of which have been upgraded with Duet electronics: Duplicator 5S Mini [DuetWifi, Bondtech QR extruder, 800mm bowden tube, E3Dv6 hotend], Duplicator i3 [Duet Maestro, direct drive Flexion extruder], Ender 5 Plus [Duet Maestro, Bondtech BMG, 900mm bowden tube, E3D Volcano hotend]). I attempted to fix the issue with Pressure Advance settings, but found that the bulge did not disappear, but rather a gap formed before the bulge when increasing the PA value - once again, tested on all 3 printers.
I am not sure whether this issue is related to Duet or PrusaSlicer - if we find it is an issue in PS, I can report it there.
Having taken a closer look at the Gcode for a few of the models sliced in S3D vs PS, I see no obvious causes or differences; however I noticed that when printing, there is a noticeable delay between the end of a layer and the start of a new layer, when PS generated the gcode. I think that this dwelling/delay is causing the bulge.
Here is an example of a layer change by S3D:
G1 X84.868 Y99.227 E0.0669
G1 E-5.0000 F3000
; layer 6, Z = 1.800
; feature inner perimeter
G1 Z1.800 F1002
G1 X83.819 Y100.429 F12000
G1 E5.0000 F3000
G1 X87.052 Y94.363 E0.4939 F3600
Compared to PS layer change (on a different model, customizable_box_try2.gcode, full file is attached, which also shows settings used at the end):
G1 X225.782 Y131.958 F12000.000
G1 E4.00000 F3000.00000
M204 S1500
G1 F2400.000
G1 X228.266 Y131.338 E0.16433
M204 S1200
; before layer change
G1 Z13.750 F12000.000
; after layer change
G1 E-4.00000 F3000.00000
G1 X145.341 Y222.207 F12000.000
G1 E4.00000 F3000.00000
M204 S1500
G1 F2400.000
G1 X139.408 Y222.214 E0.38627
PS adds the acceleration changing commands in, but I don't think they do anything related to the issue (other than M204 not having an S-parameter). I also noticed that PS adds a bunch of empty G1 commands (no parameters) when doing thin walls (as can be seen at the end of the file), but the bulge happens on all layers.
Another thing I noticed is that PS estimations are off anywhere from 50% longer to more than double the estimated time. I know it is never perfect, but still S3D was off only about 20% (and it is not like I am using outrageous speeds, or even printing way too slow).