Game freezes for few seconds every so often

In random time intervals, Minecraft takes 100% load on all cores and completely freezes for a couple of seconds. Freezes come in series, i.e. they happen more common for a few minutes and then become less frequent.

They happen in Vanilla singleplayer, no idea about multi.

Tested sound, checked if it is chunk saving and it seems uncorrelated to those.

I would put my bet on light calculation, it may be happening during sunset/sunrise and on new chunks generation, loading and refreshing. The freezes has been happening for a few versions now (since 1.4.2 I think), so it may be connected to code light fixes.

The issue seems exactly the same as MC-535. But that one was deemed "invalid" for allegedly being reported for modded Minecraft.