[VLC 2.0.8.a-1] h264 video freezes while playing

I've got a problem with every newer version than vlc-2.0.8.a-1 (current is 2.1.1-2). Almost every MKV file with h264 codec freezes a lot while playing and reports errors like this:
[0x7f5dd8001248] main vout display error: Failed to resize display
[0x7f5e14004618] main input error: ES_OUT_SET_(GROUP_)PCR is called too late (pts_delay increased to 300 ms)
[0x7f5e14004618] main input error: ES_OUT_RESET_PCR called
[h264 @ 0x7f5df4c1cc40] Missing reference picture, default is 0
[h264 @ 0x7f5df4c1cc40] decode_slice_header error
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 0
[h264 @ 0x7f5df4ce3200] decode_slice_header error
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 0
[h264 @ 0x7f5df4ce3ae0] decode_slice_header error
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65524
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65524
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65524
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65524
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65524
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65524
[h264 @ 0x7f5df4c1cc40] Missing reference picture, default is 65522
[h264 @ 0x7f5df4c1cc40] Missing reference picture, default is 65522
[h264 @ 0x7f5df4c1cc40] Missing reference picture, default is 65522
[h264 @ 0x7f5df4c1cc40] Missing reference picture, default is 65522
[h264 @ 0x7f5df4ce3200] reference picture missing during reorder
[h264 @ 0x7f5df4ce3200] reference picture missing during reorder
[h264 @ 0x7f5df4ce3200] reference picture missing during reorder
[h264 @ 0x7f5df4ce3200] reference picture missing during reorder
[h264 @ 0x7f5df4ce3200] reference picture missing during reorder
[h264 @ 0x7f5df4ce3200] reference picture missing during reorder
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 65522
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 65522
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 65522
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 65522
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 65522
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 65522
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65526
[h264 @ 0x7f5df4c1cc40] mmco: unref short failure
[h264 @ 0x7f5df4c1cc40] mmco: unref short failure
[h264 @ 0x7f5df4ce3200] Missing reference picture, default is 65530
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] reference picture missing during reorder
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 65530
[h264 @ 0x7f5df4ce3ae0] Missing reference picture, default is 65530
[h264 @ 0x7f5df4ce43e0] Missing reference picture, default is 65534
[h264 @ 0x7f5df4c1cc40] mmco: unref short failure
[h264 @ 0x7f5df4c1cc40] mmco: unref short failure
any help?

I have the same problem. FLAC files are stuttering as well, but that's already reported. It looks like it's a problem of the last update, since the old one was fine

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    com.apple.iokit.IOCDStorageFamily          1.6.1
    com.apple.driver.XsanFilter          402.1
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    com.apple.iokit.IOUSBFamily          4.2.4
    com.apple.driver.NVSMU          2.2.7
    com.apple.driver.AppleEFIRuntime          1.4.0
    com.apple.iokit.IOHIDFamily          1.6.6
    com.apple.iokit.IOSMBusFamily          1.1
    com.apple.kext.AppleMatch          1.0.0d1
    com.apple.security.TMSafetyNet          6
    com.apple.driver.DiskImages          289.1
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    com.apple.iokit.IOPCIFamily          2.6.5
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