Hello,
I have the same problem with Marlin 1.9 and Octoprint 1.9.3
The both worked great before update of Octoprint (installed in 2019).
Impossible to find the problem but mostly probable that is Octoprint.
Some News ?
Since I print everything through Octoprint, I just use that to calculate the e-steps. I mark the filament, then do the extrude from Octoprint and adjust accordingly. I'm sure if I tried it through just the printer it would come up different but all seems to be working well and the extrusions seem to be correct based on print tests. YMMV.