MKV + Subtitles = A/V Problems

[oasisAthens]

Hello my friends...I am sure that someone must know something to help me...I have a problem with MKV's . I am using the latest version of PMS with MEncoder to Transcode . So the problem is only with the MKV's with subtitles . When i have a MKV file with a separate subtitle the video start to shutter for a few seconds and then the audio is out of sync probably a few seconds + . When i load only the MKV no problem with A/V .... Any ideas ?
Thank you for your time.

[Plodolo]

I'm having the same issue. I'm not sure if its with MKVs, or whatnot but I have noticed that sometimes my video stutter and then picks up and then it doesn't match with the audio. So I hear what is being said and then the character says it. Or sometimes my video decides to just speed up and the audio has a problem catching up. So, it goes both ways.