You have to put subtitle outside MKV.

No matter if the the subtitle already embedded in MKV, it'll not display it. You have to extract it using MKVExtract tool. Hope this will help.

For those who have problem with MKV 1080p playback maybe this will help:

Use this formula: Width x Height x ReFrames = 8,388,608 or less should play fine.
You can use MediaInfo to get your ReFrames, Width and Height value.

For example:

voa-presto_x264_1080p.mkv (Short movie from Pixar)
Bitrate: 8,291 Kbps
Nominal Bitrate : 8,667 Kbps
Width: 1920 x Height: 1080 x ReFrames: 5 Frames = 10,368,000
Result: playback macroblocking/pixelating and stuttering

WALL_E 1080p
Bitrate: 9,671 Kbps
Nominal Bitrate: 10.2 Mbps
Width: 1920 x Height: 800 x ReFrames: 4 Frames = 6,144,000
Result: Playback smoothly

Here are the result I got from the net (not mine):

Batman 1920 x 1080 x 5 ReFrames = 10,368,000 (Chokes)
Bitrate = 10.3Mbps
Audio = AC3 5.1 @ 640Kbps
File Size = 10.9 Gigs

Casino Royal 1920 x 800 x 11 ReFrames = 16,896,000 (Chokes)
Bitrate = 10.5Mbps
Audio = DTS 5.1 @ 1,536Kbps
File Size = 10.6Gigs

Batman #2 1920 x 800 x 5 ReFrames = 7,688,000 (Plays Smoothly)
Bitrate = 13.2Mbps
Audio = AC3 5.1 @ 640Kbps
File Size = 9.43Gigs

Incredible Hulk 1920 x 816 x 5 ReFrames = 7,833,600 (Plays Smoothly)
Bitrate = 10.1Mbps
Audio = DTS 5.1 @ 1,536Kbps
File Size = 7.95Gigs

Hope This will help . I'll post more result if I got more time test the rest my 1080p collection.

Technically not. The Scene Release removed/cropped the top and bottom black bar. But the width they don't touch.

I think you have problem with your AV receiver. me and my friend share our mkv collection. But he have problem with some mkv with dts especially dts-es. It will clipping every 5 seconds but not me. The only file I have the same problem right now is Band Of Brothers mkv (dts).