If you're on an MVP, it could be related to the new version of the Hauppauge file dongle.bin. The new version which is included with v0.90.x works well with the new 45 button remote, and supports the new "fully transparent OSD" option, but I have noticed it's a bit quirky with the old 34 button remote when video is playing.
If you've got time, you could try going back to an older version of the dongle.bin to see if it helps, but make sure your disable the  "fully transparent OSD" option.
As it is now, I see white numbers appear on my TV screen when pressing on the control but disappear quickly before I press "OK". Is this the normal behavior?