Any problems with DVD playback codecs are because CCCP includes it's own codecs for MPEG-2 playback (which work quite well on my systems), and which are set as the default when you install CCCP. Just like everything else, whenever you install a new codec, they tend to "take over" playback of the media types they support. CCCP actually lets you easily disable this for most of the common types in it's settings. Check the options during the install process.
After the fact, if you want to keep your own MPEG-2 DVD decoders as the defaults for DVD playback but use CCCP for everything else you can easily manually increase the priority of the codecs that got "shoved to the back of the line".
There are two ways to do this:
1) reinstall whatever codec/application it was that got usurped (WinDVD or whatever)
2) use a DirectShow filter manager, like
Rad Light, to increase the priority of the codec that isn't being used. This is a little more complicated, but if you have questions just ask and I'll explain (do a search here first for Rad Light because I've linked instructions before).
I would also mention though that I've done some serious testing and generally the codecs in CCCP outperform those in WinDVD and PowerDVD by a fair margin when used from within MC. FFDSHOW most certainly does support AC3 audio, dolby surround, and all that good stuff. I'm not positive about DTS (you could certainly ask on the CCCP forums). Keeping the WinDVD filters isn't a problem if you like them. I don't, but YMMV!