Layer shift in Repetier-Server, but fine in Repetier-Host (no replies)

I have been successfully printing with Repetier-Host for a few months now with a Folgertech Prusa i3 2020 using Marlin firmware.
Just recently I tried to use Repetier-Server to control the printer remotely. Setting up the server went pretty smoothly and I am able to connect to the printer, send commands, execute a print, etc. But my prints have errors where a layer will begin in the wrong location, and from there on the print is incorrect. This happens when printing from Repetier-Server as well as Repetier-Host (when connected through RS). But if I connect Repetier-Host directly to the printer (serial connection, using USB ) it prints fine just like it has been for the last few months. The preview in Repetier-Host (again, connected thru Repetier-Server) looks correct, the gcode file is correct when examined in a gcode analyzer. But RS keeps printing with the layers shifted. And it is not repeatable, I printed this same part a few times and the layers shifted at different Z locations.
The connection settings for Repetier-Server are the same as those for Repetier-Host, when Host is connected directly to the printer.
Does anyone have any ideas? Thanks