Quality will be identical between Quicktime "Official" and Quicktime Alternative. QT Alternative simply provides DirectShow filters to allow DirectShow players like MPC, WiMP, and MC to play back the files (without having the real Quicktime Player installed). Same goes for RealAlternative (and I completely agree -- I'd never have Real installed on any of my systems). Quicktime isn't quite as bad IMHO (though I don't like iTunes and it's system services), but the QT Alt is just as good and not evil at all.
I happen to own Quicktime Pro, and use Macs a lot so I keep the "official" package on my machines.
As far as actual MP4 and M4A playback, I'd probably stick to FFDSHOW if it's working. I use Haali as my splitter instead of MP4Splitter. YMMV. I like the new beta builds of Haali (included with CCCP's Betas as well). Yaobing (one of the main developers of MC) tends to like MP4Splitter better. To each their own!
Having Quicktime or QT Alternative will help though, as MC will "detect" that QT is there. MC uses Quicktime as the "fall back" if playback fails for many MPEG-4 media types.
Since your playback works properly, but gives the error with second file, I suspect that this is a bug that needs quashed. However, to solve it for you in the interim, I bet that installing QT Alternative will make it go away. The other possibility is that your second file happens to be "broken" in some way that's preventing MP4Splitter or FFDSHOW from rendering it. I assume that you've tried "starting play from scratch" with some of the same files that cause the error though when played "second" (and if so, then obviously they're not broken)...
You might have to re-set FFDSHOW's CODEC page options to tell it to use libavcodec for MPEG-4 decoding again after you install QT Alt (not sure).