It shouldn't be any different. Are you using run external to call toDVRMS in your "\recroded tv" folder process?
sccrgoalie1 - sorry, am not sure I understand your question. I currently have DVRMSToolbox filewatcher set to scan both my \tvtemp and \recordedtv folders. \tvtemp is where files are placed in MKV format to be converted using the 'convert mkv to wtv' profile. \recorded tv is where wtv files reside simply to be fed to showanalyzer for commercial scanning.
I am able to successfully drop a .mkv file into \tvtemp. and the 'convert mkv to wtv' profile executes (command line of -wtv -v), the tvdb.org data is found (an thus an xml is generated alongside the mkv). after the mkv is converted to an wtv, my 'convert mkv to wtv' profile deletes the input file (in this case the mkv) and moves the resulting .wtv output to \recorded tv. this has worked for me in the past on another system though perhaps I am overlooking something obvious?
the good news is that the mkv is being converted to wtv as expected (automatically) however the resulting wtv stutters and upon hitting FF/RW immediately audio and video fall out of sync (and never recover) or after allowing the wtv to play it will ultimately begin stuttering.
If instead I manually launch the GUI and select input (mkv file) and output file locations and the 'convert mkv to wtv and click RUN, the process kicks off and completes normally and the resulting wtv is PERFECT.