Hey @shurik... I swear I see this thread for the very first time! I see, you feel like that again (sorry, I couldn't resist... ):
It happens I just had to play around with the one-at-a-time feature... to me the gcode looks fine. There is a G92 E0 (zeroing the extrusion), then a G10 (retraction), then only G0s without extrusion, then a G11 (priming) and then reasonable numbers for the E-coordinate.
Maybe something bad happens in Marlin. If (for whatever reason) the G10 is executed before the G92 E0, one would exactly get the issue you seem to have.
To be honest, I rarely print more than one object in one print job and if I do, I print it all at once to have reasonable layer times. That doesn't mean you're doing something bad but I just do not have experience with it...