I familiar with all three of the tools mentioned. However, I haven't found any of them to be that reliable.
MpegRepair only works on Transport Streams and is very slow. Sometimes I'll use this before DGIndex. This is probably the most promising solution. I need to do some research on the log file it creates.
VideoReDo Plus isn't free.
However, I have had some success using this for some DVR-MS files but they still had delay sync issues. Also, I can't remember exactly how it handles glitches, but I think it just drops the GOP.
ProjectX usually doesn't play nice with my hd recordings and I think it also drops the GOP rather than replacing with blank frames.
Is it true that transport streams just don't have reliable global timestamping that can be used to easily determine this information?
Also, those glitches didn't play well with the telecide().decimate() I was doing. I had to work around by trimming each section individually before the telecide().decimate().