First im a newb, no expert

But i also had this problem with some [not all] MKV files "out of sync video/audio"
I allmost gave up trying to convert them,
untill i realized you can off set the stream on them

fix it by.....
first add mkv file

Click on the file you added
Go to .....Source Details :

Go to where you see ....Stream Count
You will see something like this....
#1 - Video
#2 - Audio
Ok double click on video, or audio
[one or the other, not both - I think i offset the video on mine]
and offset it to...... -3ms or mabye -2ms

Do a few test to see what works better

It converted it fine for me...worked perfect

One Thing i never had any problems with "high pitched sound"
Converting mkv files... for this problem i cant help

good luck