I'm getting the exact same error when I try to play a certain .mkv file on 1.1.11 at the same point every time. As soon as the video reaches 6:30 I get the same popup and then vlc crashes after I hit okay... I tried backing down to 1.1.10 but it didn't fix anything...
Windows 7 Home Premium 32-Bit
It looks like ind the Windows Error Log it's the libmkv_plugin.dll that's causing the problem:
Faulting application name: vlc.exe, version: 1.1.12.99, time stamp: 0x4e52f3a9
Faulting module name: libmkv_plugin.dll, version: 0.0.0.0, time stamp: 0x4e52f3af
Exception code: 0x40000015
Fault offset: 0x000771a1
Faulting process id: 0xac8
Faulting application start time: 0x01cc621d413fc3be
Faulting application path: C:\Program Files\VideoLAN\VLC\vlc.exe
Faulting module path: C:\Program Files\VideoLAN\VLC\plugins\libmkv_plugin.dll
Report Id: 9bdb77c9-ce10-11e0-a6da-001eec852463
Also:
Faulting application name: vlc.exe, version: 1.1.10.0, time stamp: 0x4dec1ec0
Faulting module name: libmkv_plugin.dll, version: 0.0.0.0, time stamp: 0x4ded62f2
Exception code: 0x40000015
Fault offset: 0x00078781
Faulting process id: 0x628
Faulting application start time: 0x01cc621adc57c0f0
Faulting application path: C:\Program Files\VideoLAN\VLC\vlc.exe
Faulting module path: C:\Program Files\VideoLAN\VLC\plugins\libmkv_plugin.dll
Report Id: 332a01e4-ce0e-11e0-a6da-001eec852463
And again:
Faulting application name: vlc.exe, version: 1.1.11.0, time stamp: 0x4e1edf37
Faulting module name: libmkv_plugin.dll, version: 0.0.0.0, time stamp: 0x4e1edf3e
Exception code: 0x40000015
Fault offset: 0x00078701
Faulting process id: 0x80c
Faulting application start time: 0x01cc621978bd22ea
Faulting application path: C:\Program Files\VideoLAN\VLC\vlc.exe
Faulting module path: C:\Program Files\VideoLAN\VLC\plugins\libmkv_plugin.dll
Report Id: be6dc888-ce0c-11e0-a6da-001eec852463