First suggestion is to eliminate the Onkyo AVR and connect directly to your TV. Do these problems still exist with your HTPC or Roku?
Have you tried using the actual remote for the Roku and a keyboard/mouse for the HTPC to control them?
Are your drivers up to date for the HTPC? Windows current with updates?
Is the Roku firmware up to date?
Get back to us with some answers so we can help you cont. to troubleshoot.
Denon AVR-3311CI, Denon DVP-602CI, B&K Reference 200.7 S2, Belkin PF60
Sony BDP-S5000ES, Silverstone HTPC (6 Tuner DVR & 10 TB Media)
PSB Stratus Minis, PSB Stratus C6, PSB Alpha S surround, James Subwoofer EMB-1200
Sharp LC-70LE755U, Harmony 880 Remote