I also had problems with smooth playback when I got my new 1080p projector. I thought it was strange, since both 720p and 1080p files stuttered, but played fine on my 1360x768 LCD tv. I thought it was because I couldn't get the ATI card to output 23.976, only 24 Hz. Using MadVR it was totally unwatchable EVR stuttered about once every half minute or so.
Anyway, enabling decoding and exclusive mode in MadVR did the trick for me. RO HQ selected in MC. Now I can watch a whole movie without any stuttering, using a Core2Duo E6300 running at 2.66 GHz (OC'd from 1.86). Had a ATI HD4550 card, now I have a HD6850, but no difference between the cards in my case. Still stutters with my previous settings.
Btw I don't use Videoclock or Reclock, and have HW deconding on. The HW decoding setting makes no difference when using MadVR with ATI/AMD. Does not allow MadVR to change refresh, using 24 Hz setting in Catalyst Control Panel.