I've got a similar problem on a LC (not R and not remapped). Mine's a bit less time dependant though as the boost will just drop off completely at any stage in a journey. What happens with mine though is that if I stop the engine and re-start straight away the boost is back to full again no problem. That makes me think it's not temperature but is more likely electronics (sensors / ECU etc).
Does switching yours off and on again cure it or is it still lacking boost when it comes back on? If that is the case then it does sound temperature related doesn't it.
I've not tried disconnecting the battery on mine though, will do that tonight.
Mines is the exact same, been remaped with standard pipes, thinking of replacing them and the DV to see if that sorts it.
Still need to check vag-com to see what error codes i am getting.