Using both my standard and testing installs to make tests to various 1080p files, I can safely say that the problem is not general; some of the files play well and some of them don't. Some play better in Smplayer and not at all in VLC and vice versa. I only use those two players as they seem to work best for me of all I have tried (XBMC also has good performance). Test system uses Catalyst 12.6 from ATI's site and no Pulseaudio and my standard system uses Catalyst 12.4 from repos and Pulseaudio. I'm not certain, but I have suspicions that Pulseaudio may have something to do with this in some cases...
Hmm... you may just have some files with really bad encoding - a few rotten apples don't spoil the whole barrel in this case, though. If there are specific files that have performance issues, it might be best to attempt to transcode them to another format, or to try to obtain them in a better encoding?
Could you point me at some of the files that are giving you trouble? It might also be worthwhile to run Mediainfo on them and see what their CRF and color depth settings are looking like.
I use SMPlayer primarily, but I find Xine works better for some things and worse for others when compared to SMPlayer. I toyed with VLC for a while and found it had too much overhead for my little laptop to handle well.
If your CPU supports hyperthreading, then a dual core will present as though it were four virtual processors, so try jacking up the number of threads a bit higher. Hey, it'll either work or it won't.
Do the troublesome files originate with Youtube, by any chance? If so, you might try the Minitube viewer, or transcode them with VideoDownloadHelper (it's a Firefox add-on).
The bit about pulse audio being part of your problem? What would make you tend to suspect that? I've heard folks say this before, but it usually turns out something else was actually wrong... (I'm definitely no expert on Pulse Audio.)
I'll be curious how it turns out for you with higher cache settings and more threads.