Thank you @Claudia-Frank ! I think the code you point to is indeed where the problem occurs.
I am not sure about the intricacies of NpptoR, but the plugin manages to take lines, selections and scripts in N++, and pastes and/or executes them in the R console window (so not in the N++ window like nppExec does). I’d like to learn how to apply nppExec for R, but it would probably be best to leave that for another time :)
The issue is mentioned here at SourceForge and here at Github but the bit of code you refer to does not seem to be identified there, so thanks a lot for bringing it up.
I hope it will come to the attention of the NpptoR developers, unless the N++ developers revert this part of the code as you suggest elsewhere.