.WTV file transcoding - occasional issue

I am trying to stream OTA HD signals from my PC to a WDTV Live. The files are created by Win7 WMC. Generally, everything works fine, but occasionally some files do not transcode. I used the debug log to look at the ffmpeg command and I ran it in a command prompt. I found that occasionally I got an error relating to genpts. After some searching around this forum and the web, I found that the solution is to add the following flags to the ffmpeg command line; "-fflags +genpts".
This problem was apparently fixed in a previous version according to this tread viewtopic.php?f=3&t=665&start=10, but my 6.0.1 does not include those flags. Could it be possible to add them? Also, in the interim, I wanted to use a .bat file to just add the flags manually, but since Serviio specifically calls ffmpeg.exe, I cannot do that. I tried to compile the bat, but that didn't seem to work well. Does anyone have a solution?
This problem was apparently fixed in a previous version according to this tread viewtopic.php?f=3&t=665&start=10, but my 6.0.1 does not include those flags. Could it be possible to add them? Also, in the interim, I wanted to use a .bat file to just add the flags manually, but since Serviio specifically calls ffmpeg.exe, I cannot do that. I tried to compile the bat, but that didn't seem to work well. Does anyone have a solution?