r7483 x64 (MAMARIO)
r3.0-397-x64 (emucr)
Has the same problem tested with many config.

More info can be found here: http://forums.dolphin-emulator.com/showthread.php?tid=1413&pid=196391#pid196391

Curios, because on my rig this black border issue is different.
I have this black border in Metroid Prime Echoes with all newer
revisions for such a long time that I can´t remember if it ever
worked without the border... However, I tried "r6505" as
BurnHellXP suggusted and yeah, no black border o_O
The difference to burnhell's explanation of his problem and mine
is that the black border ALWAYS consists from the beginning
of the game (Excluding the game menu... there is no such border!),
so on my system the lags don´t cause the black border... it's always there.
Waiting for fix, so long... I already tried different Resulutions,
different Aspect Ratio's, Render to Main Window, Crop, Widescreen Hack, etc.

Additional information:
I use Windows Vista x64.
I use the OpenGL graphic backend.
Tested 3.0-419 (x64) --> Black border.
Tested r6505 (x64) --> No black border.
Metroid Prime 2 Echoes \G2MP01\ 2004/05/21 \PAL (Europe).

What "other games" have this problem? I was able to reproduce this issue in MP2 when testing Issue 5448 but would like to see if other games work better on revisions after about 6523 because MP2 gets crash prone. Also do any of you have this problem if you disable duel core? I have not. For others testing this problem its important to delete your shader cache. This problem goes away after a while if you dont(at least for me)

2xOpteron 256, Radeon HD2600XT(512MB agp), 2GB ram, win7prox64

captg...@hotmail.com, the black bar appear even with the shader cache deleted and like you said "other games" are Sonic Adventure 2 Battle PAL and maybe others.

http://forums.dolphin-emulator.com/showthread.php?tid=35&page=12

Like pauldacheez said on Issue 5448, when all models or textures that aren't nailed to the floor as part of the map geometry disappear for a split-second, then reappear, the black bar will appear.

After Issue 5448 get a fix, the black bar issue will probably be fixed too

If you disable dual core does the problem go away for you in MP2 and Sonic? I don't have Sonic to test.

Does the black bar in sonic go away if you enable XFB Virtual? Does the screen flicker when you do?

Yup confirm this stuff

OGL seems unaffected
DX9 & 11 slill remain issued
Issue doesn't care about scaling it's good, and Virtual XFB seems helpful, but causes flickering

This issue like the Issue 4336, like many other CP/Fifo issues had startd with
r6554 - ra9ca9cfd9bc8
Sometimes this game starts with blackscreen and sound, requires to resize the windo manually or erase game's Shader Cache, harmless but very annoying

This issue has now been fixed by an unknown revision.
Been playing for over three hours and theirs no black bars or micro stuttering

Issue is still present for me.

Tested with rev3.5-1769 on Win8.
Tried using both the Dx11 and OGL backends on default settings, still getting black bars several minutes in.

D'oh. Forgot to mention I tested on MP3 NTSC. Since the issue says other games, I'm assuming MP3 was to be included in this issue also.