Thanks for the sample. It appears that the original video has a lot of timestamp corruption (likely caused either by a bad OTA signal or a tv tuner driver issue which could be addressed if it’s a problem by trying a different tv tuner driver version or amping up the OTA signal).
There was a bug in MCEBuddy where it failed to properly detect the corruption and so it would end up ignoring the corrupted video. We’ve fixed that in the latest 2.6.5 beta version. Now it will detect the corrupted video and if it can’t make the cuts prior to conversion, it will try to correct the video issues during the conversion and then try to cut the commercials out after conversion. When this happens it will take longer to process the conversion but it should be able to recover the video and cut the commercials successfully.
Try out the latest beta build and let me know how it goes.