Hi Faktar,
Here's my ten pennies worth for what it's worth, could be the expansion of the gears and pinions, the tolerence is much closer when the engine is hot.
Also when the oil is cold it tends to muffle noises more than when it is hot.
Mine sounded to more noisier when hot but when I pulled the motor apart every thing was how it should be. This engine has also had new crank piston and bearings recently.
The reason for strip down was it kept partially jumping out of third gear, somebody had reassembled the shims wrongly on the counter shaft.
Regards
Sparks.