Apologies for reviving this dead thread but thought it might help another.
This issue persisted off and on for the last year, and got worse. At the same time the original starter had developed a shrieking noise while cranking. The shrieking noise became more regular as the starter was obviously wearing out. Recently, I had the starter rebuilt by an independent rebuilder for $95.00, and have not had the starter noise OR the low, rough idle and stalling following startup since. According to my guy, when the starter wears to that point it doesn't crank the engine fast enough and will cause the idle/stalling issue until the engine catches up after a few seconds. Very common for the 2.0L VW he said.