...It's been bugging me for years and I've not found a suitable work around.
There is one obvious workaround which will solve it much of the time, but the downside is it adds another step to your workflow.
When I want to upload an ident onto my YouTube channel and have the capture imported in Premiere Pro, in order to tidy up the start and end points, add my DOG
etc, if there's an audio problem at the head of the ident, I just import another of my captures of said ident, use the first second or so of its soundtrack and crossfade over just past the problem point.
Mind you, I don't have to worry about the countless channels you cover in TIG
, just BBC1 and BBC2, mainly for me, at the moment.