I have seen the "!" problem in every PGN mail I have received. The first of these was on 29.01.2004, before the recent (and very welcome) changes to the PGN output.
Something that does seem to have started with the recent changes is that sometimes there is a spurious '=' sign at the end of one line and a letter 'A' at the start of the next.
I have amended my Perl script to filter this noise out; I'm also planning to fix up themed tounaments by supplying [SetUp="1"] and [FEN=...] tags. (I might even try to calculate min, max and average move times for each player, but that's another story.)
Of course the script will have have a hard-coded look-up from tournament names to their FEN strings, so it would better fixed at the RHP end. Nonetheless, if Russ or Chris are reading this, I'd rather see the development effort spent on a 'removed pieces' sidetray in the Analyse Game screen.