Audio out of sync after cutting scenes from an MKV file with Avidemux

[kr1ge]

I have been cutting a few scenes from an MKV file using Avidemux 2.5.3. I have done so, as I have read somewhere, only from keyframe to keyframe using the << and >> buttons in Avidemux (is it normal they all are exactly every 10 seconds?). Also when opening the file I got the following confirmation dialog:

H.264 detected
If the file is using B-frames as reference it can lead to a crash or stuttering. Avidemux can use another mode which is safe but YOU WILL LOSE FRAME ACCURACY.
Do you want to use that mode?

To which I answered NO. And then another confirmation dialog:

Index is not up to date
You should use Tool->Rebuild frame. Do it now?

To which I answered YES.

When saving I set the options:

Video: Copy
Audio: Copy
Format: MKV

The resulting file appears to be almost completely fine but there are some scenes (from a keyframe to another keyframe I noticed) in which the audio is out of sync. In a 6:30 minutes long file it happens only once, from 5:30 to 6:10, and in another 10:00 minutes long file it happens twice, from 2:10 to 2:40 and from 8:30 to 8:50.

Does anybody know where could be the problem and how I can fix it?

[kr1ge]

Problem solved.

The source file was actually a MOV produced by a Canon S95 camera: I then converted it to an MKV using Handbrake.

I tried instead converting the source file to an AVI using XMedia Recode; I then edited the AVI using VirtualDub and everything went fine.