When MC is set to do TV recordings in TS format, it doesn't convert the JTV files to TS at the end of the recording. It saves the TS files directly during the recording. You probably don't see them during the recording as they would be temporary files until the recording was done. The JTV files and directory are just used for Time Shifting in that case.
So if the TS files are not turning up once the recording is finished, something is going wrong with your recordings. Either they aren't starting, or aren't finished yet, or the TS files failed to write to disk. Or I guess maybe you just can't find them. Use the "recent" view in TheatreView to find recently completed recordings. If directories containing JTV files are being left behind after a recording session and the Time Shift time has passed, then something is wrong. There have been some issues with JTV directories being left behind instead of being cleared up recently. Maybe what you are seeing is related. Some of that problem was supposed to be fixed in MC20.0.21, but those fixes were related to watching TV on a MC client rather than a server. If you are using a client, this could be related to your problem.
MC does have a utility to convert video and audio to new formats, but it will only save stereo sound, not 5.1 channel sound commonly available in recordings. It has a limited range of predetermined file format profiles to choose from. It will convert from JTV to another format though, and even to TS formats. You must run the conversion on the server, as it won't be an available option a MC client, the option will be greyed out. Find the recording in Standard View, however you prefer best. I use the Video > Files drill down usually. Then either Right Click on the recording and select Library Tools > Convert Format, or select Tools > Library Tools > Convert Format from the menu.
If you would like to have the benefits of recording using the JTV, and then be able to convert recordings into a single file, while also trimming the end and cutting out commercials, get over to this thread and add your support:
http://yabb.jriver.com/interact/index.php?topic=92571.0