I am having the same problem.. I can play some .mp4 in my TV section but none of the .mkv files in any section play using either the centre button or the play/pause button. Apple tv is running the latest firmware. Let me know if you need any more details.
Here is the terminal output where I successfully played an .mp4 in my tv section including some fast forwarding, pausing etc. followed but an unsuccessful attempt to play an .mkv in my movie section. The ATV displayed "An error occured loading this content. Please try again later.
10.0.1.2 - - [06/Jun/2013 12:55:40] "GET /library/metadata/8084&PlexConnect=Play&PlexUDID=DCYGRHZLDDR5 HTTP/1.1" 200 -
ATVLogger : Player state: Loading at this time: 0
ATVLogger : Player state: Playing at this time: 0.08
DNSServer : DNS request received!
DNSServer : Source: ('10.0.1.2', 60563)
DNSServer : Domain: trailers.apple.com
DNSServer : ***intercept request
DNSServer : -> DNS response: 10.0.1.3
ATVLogger : Player state: Paused at this time: 9.072976861
ATVLogger : Player state: FastForwarding at this time: 9.263777777777777
ATVLogger : Player state: Paused at this time: 9.448094655
ATVLogger : Player state: FastForwarding at this time: 9.555722222222222
ATVLogger : Player state: Stopped at this time: 0
WebServer : serving .xml: /library/metadata/8082/allLeaves
10.0.1.2 - - [06/Jun/2013 12:56:11] "GET /library/metadata/8082/allLeaves HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/updateXML.js
10.0.1.2 - - [06/Jun/2013 12:56:11] "GET /updateXML.js HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/scrobble.js
10.0.1.2 - - [06/Jun/2013 12:56:11] "GET /scrobble.js HTTP/1.1" 200 -
WebServer : serving .xml: /library/metadata/8082/children
10.0.1.2 - - [06/Jun/2013 12:56:28] "GET /library/metadata/8082/children HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/updateXML.js
10.0.1.2 - - [06/Jun/2013 12:56:28] "GET /updateXML.js HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/scrobble.js
10.0.1.2 - - [06/Jun/2013 12:56:28] "GET /scrobble.js HTTP/1.1" 200 -
WebServer : serving .xml: /library/sections/3/firstCharacter/A
10.0.1.2 - - [06/Jun/2013 12:56:29] "GET /library/sections/3/firstCharacter/A HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/updateXML.js
10.0.1.2 - - [06/Jun/2013 12:56:29] "GET /updateXML.js HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/scrobble.js
10.0.1.2 - - [06/Jun/2013 12:56:29] "GET /scrobble.js HTTP/1.1" 200 -
WebServer : serving .xml: /library/sections/1
10.0.1.2 - - [06/Jun/2013 12:56:38] "GET /library/sections/1 HTTP/1.1" 200 -
WebServer : serving .xml: /library/sections/1/firstCharacter
10.0.1.2 - - [06/Jun/2013 12:56:40] "GET /library/sections/1/firstCharacter HTTP/1.1" 200 -
WebServer : serving .xml: /library/sections/1/firstCharacter/A
10.0.1.2 - - [06/Jun/2013 12:56:42] "GET /library/sections/1/firstCharacter/A HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/updateXML.js
10.0.1.2 - - [06/Jun/2013 12:56:42] "GET /updateXML.js HTTP/1.1" 200 -
WebServer : serving /Users/Mini/Desktop/PlexConnect/assets/scrobble.js
10.0.1.2 - - [06/Jun/2013 12:56:42] "GET /scrobble.js HTTP/1.1" 200 -
WebServer : serving .xml: /library/metadata/418&PlexConnect=Play&PlexUDID=DCYGRHZLDDR5
10.0.1.2 - - [06/Jun/2013 12:56:45] "GET /library/metadata/418&PlexConnect=Play&PlexUDID=DCYGRHZLDDR5 HTTP/1.1" 200 -
ATVLogger : Player state: Loading at this time: 0
ATVLogger : Player state: Stopped at this time: 0