HT-C655W input/output combination causes playback issues

I recently purchased a samsung series 6 led TV and this HT system. At the time of purchase i didn't have an HDMI cable to enable video so i simply used the HT as an external sound source for the TV by connecting through toslink cable and setting the TV audio to external speakers.

Today I purchased an hdmi cable and connected it to the tv, enabling anynet+ in the process. When playing a DVD i noticed that the rear speakers had their volume fixed to what was first set when dvd playback started, regardless of what I set the master volume to. I also noticed that the controls on the HT were very sluggish, taking several seconds to respond to volume changes and even longer to certain other commands. This sluggishness persisted even after I stopped the DVD and returned the source to the TV. On turning the HT off and on again (I had to use the touch button on the unit since it wouldn't respond to the remote power button, and the unit made a strange sounding and longer than usual beep when turning off) the "HELLO" message slowly crept across the display and the wireless rear speakers didn't connect at all (still showed the red standby light).

My suspicions were that this was caused by the particular combination of optical connection for tv audio to HT, HDMI connection for HT video to TV and CEC connection for TV remote to HT. I tried to turn the TV back to having internal speakers and setting the HT to output audio through HDMI, but i couldn't change the TV audio settings back to internal until I turned the HT off.

Setting the TV to internal speaker fixed the sluggish response issues and subsequently returning the HT to using its own speakers for DVD playback also works fine. One issue remains though - whenever the HT is on, the TV forces itself to external speaker unless the HT is set to AUX input (as opposed to D/IN), even if I don't have the optical cable connected. This doesn't cause the other issues mentioned above to come back, however this will be an issue when the BD player from the samsung promotion arrives and i use the optical audio with that, since the HT only has one optical input and hence I would prefer the TV to remain on internal speaker always.

TL;DR? Short version: major software issues with samsung TV, HT combination which I managed to work around but default samsung device interoperability seems to be annoying even though it's obviously trying to be clever.