Editing video files (in Linux)

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A long while ago I ripped some DVD discs into the various VOB files and then concatenated them (using cat 1.vob 2.vob ... etc) into a single file, which I also gave the extension .VOB, following advice from some forum thread. However, the files do not play on all devices (specifically, they have missing sound, out-of-sequence skips or cycle back to the beginning at some point on a hardware mediaplayer), but they do play absolutely fine in VLC or similar software, except that the total film length is incorrect (too short).

I am guessing that the one big file contains DVD chapter marks that refer to the original VOB, but are incorrectly interpreted by the hardware mediaplayer within the big file (e.g. playing the wrong audio, or continuing forward actually skips back).

Is there any good method of fixing these errors? (Before anyone asks, they are not encrypted and include such delights as First Holy Communion, for which I no longer have the camcorder tape).

And one other thing, in addition to deleting the chapters / cells or whatever causes playback to loop.

In a couple of the files, I have an empty audio stream before the real audio stream. I assume that it was created by my DVDR mistakenly recognizing either an alternate audio stream or alternate (e.g. 5.1) format that didn't actually exist.

What video editing software (in Linux) manages multiple audio streams, so that I can delete the first one, or change the order?