Converting .WTV Files

Hi Guys,

I have almost 2TB of recordings from the just finished TV season and am now looking to convert them to .MKV for storing. These were OTA recordings done in the highest quality setting in WMC. I had started off with a few files in Handbrake and they came out looking fine, but the next 3 I tried and randomly stopped at various percentages. I tried each of them multiple times and they would always stop at the same point as the last time. i.e one would stop at like 24.14% every time, another 89.72% every time, etc. Same settings were used during times when it worked and didn't. Could it have perhaps been to an interruption in the video feed due to interference during the initial recording? I know not all of the recordings were perfect all the time, but it's hard to tell from the original video what would have cause it to stop. Is there something I should be feeding the video through before Handbrake? Not using Handbrake at all? I know a fair bit about conversion, but the easier the process, the better as I have almost 400 recordings to go through.

Any and all help is greatly appreciated. Let me know if more information is needed.

Thanks