Sorry for misunderstanding, I thought that question was about Ubuntu
installation. Openshot was installed from Ubuntu repos, not from usb
stick.

Anyway, I managed to solve the problem. It was because of melt/libmlt, I had 
the same issue in kdenlive.
melt was unable to correctly process "Audio: pcm_u8, 11024 Hz, 1 channels, u8, 
88 kb/s" audio format.
I converted the sound stream for all videos it to "pcm_s16le, 22050 Hz, 1 
channels, s16, 352 kb/s" and glitches are gone!

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https://bugs.launchpad.net/bugs/1130920

Title:
  audio glitches when trying to play

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