Are you using 3.4 beta2 on both the mainboard and toolboard now?
Can you tell if it's only gap fill that is behaving like that?
What speeds do you have set in this macro?
; Accelerations and speed
M98 P"/macros/print_scripts/setup_printing.g"
What do you have in M98 P"/sys/print_start.g"?
I note from your gcode file that the gap fill sections have very small extrusion amounts.
;TYPE:Gap fill ;WIDTH:0.237375 G1 F4800 M204 P1000 G1 X211.402 Y165.503 E0.00282 G1 X211.393 Y165.494 E0.00018 G1 X211.122 Y165.228 E0.00559 G1 X210.850 Y164.963 E0.00559 G1 X210.842 Y164.955 E0.00017 G1 X210.587 Y164.674 E0.00558Have you tried a different slicer to rule that out?
And finally, have you tried firmware 3.3 to see if it's the same there?