I have a similar problem with my Scirocco which has a Mk2 Golf KR lump (16v GTI) engine..
Battery drains about 0.4v daily on mine - get a voltmeter and measure the voltage across the battery terminals when its standing as well as when the engine is running.
As DarnPB stated it should be 13.8v to 14.4v when running and 12.4v+ when standing (thats 75% charged)
http://www.iol.ie/~kilkennyhockey/BentleyManual/EE01/ch4.1.2.htmlMine has a problem starting on cold start only the first time for about 15 second it cant idle properly and sometimes dies.
I would say with the clock issue and the fact when you throttle it is ok its not a starter issue as it does start.
To check for a parasitic drain (battery draining when the car is standing) leave the car standing for a while without use and check the voltage once a day.
Also its worth checking to see if the battery is duff. Charge it full using a battery charger and leave it out of the car checking its voltage daily also.
If you're still having problems you're in the same boat as me..
If you like you can have a read of my thread to see if any of it is useful:
http://www.golfgtiforum.co.uk/index.php?topic=101482.10