I've encountered just the same problems. I've tried a variety of encoders and editors in endless combinations, but none has been able to produce a media file suitable for archiving in anything like a realistic time frame. It's just not worth spending hours on a programme you will probably only watch once anyway, especially when there are people out there (cough) who are only too happy to compete to see how quickly they can do the job for you and post the results in nice accessible places.
Freemake usually (but not always) manages to recode the Hummy's .ts files to mkv without suffering the audio problems you've met with Handbrake. It also has a built-in editor, not unlike a crude version on VideoRedo. The editor doesn't work for me, but you may have better luck if your PC can use its graphics card for decoding - mine's too old. The mkv file can however be trimmed with SolveigMM AVI Trimmer+MKV. Both of these are free and usually work, but they are long, tedious procedures.
Last time I looked, VideoRedo TV Suite H264 could edit the unwanted junk out of a Hummy ts file, but the only reliable save option was back to ts - all other 'save to' options would lock up or crash. The edited ts file is, however, recodable with Handbrake or Freemake, provided you've taken all the odd audio elements out - channel ident, ads, etc. As you say VRD is an option that comes at a price - one I'm not prepared to pay for a not-very-reliable beta version.