The only reason I can see you might need to use ARC at all is because you don't have a separate Cable or Satellite box for viewing TV. Is that why you are using it? Otherwise, there's no reason to use it w/ your current components. If so, turning off anynet (which has been suggested) is your first step. Turn off all the extra 'stuff' from both Panny & Sammy to see what happens. Otherwise, you could try a digital optical cable (output) from the Panasonic into the Samsung HT (input).
Regarding reading digital video files from DVD, it's quite normal for certain types of burned (and even commercial) DVDs to simply not play. Much more common when you burn various types of digital video files to a blank DVD then playback on your HT system DVD player. The end run now is to simply utilize a HTPC, or player such as a Roku or WDTV Live which does not make you deal with the inconsistent DVD specification.
You might instead copy your media files to a large USB drive or SDHC card. It seems as though your media player is quite the swiss army knife- much like my WDTV Live is, but with even more options. Nice. Specs for all who are wondering-
Connectivity options if ARC still doesn't work for you (hint: typically the components need to be the same brand for it to work well at all). Separating the audio output so you don't need ARC might be the ticket ;).
Samsung HT (HDMI out) --> (HDMI in) Pansonic HDTV
Media player (HDMI out)--> (HDMI in) Samsung HT
Panasonic HDTV (digital optical out) --> (digital optical in) Samsung HT
Let me know if it works. Otherwise, we can try something else.
I own a panasonic tv (et60) and a samsung home theater system (HT-F5500) that both support arc.
I have connected them properly (hdmi out of the HT on the HDMI2 port of the TV which has ARC), enabled all options (on home theater the Anynet+ is enabled ans so is the "ARC" option and on the TV the Viera link is Enabled) but i can not get any sound through the ARC.
At first i was suspicious that it may be the hdmi cable fault so i ordered a new one (high speed, 1.4 and ethernet compatible) to change it. To my surprise even with the new cable i got no result.
From both panasonic and Samsung support i did not get much help (they both say the same things about probable incompatibility of the TV/Home Theater).
Lately trying some dvd's on the HT system i say it could not access data dvd/cd that contained media files (avi, mkv and music mp3/wma) though it played dvd-video and bluray-video discs without problem (from Samsung support said it must be a "finalization" problem on the disks but i've tried plenty of them and always get the same error. Also the Viera link on the TV works as i have succesfully connectet with it to my media player and controlled using the TV-remote.
Could it be the Home theater needs service? Could it be something i have forgotten or not tried? Any help is much appreciated.
-TV panasonic ET60
-HT samsung HT-F5500 connected to TV with ARC
-Media player MEDE8ER med600x3d connected to TV through HDMI and to the HT using optical cable.