I have recently started having a problem with cold starts. The engine will crank for longer than normal and then sometimes run rough when it starts.
Normal start is less than 3 seconds, so when I recognise that it is cranking too long, or is running rough when it starts, I immediately turn off the engine and restart. The restart is always completely normal (starts within 2 seconds and runs normally). When it first started this issue, I took it to my mechanic who did a major maintenance (plugs, filters, etc) and also added a can of 44K fuel system cleaner. But, the problem persists. Any ideas what this might be caused by? 2005 A6 4.2 Quattro 102,000miles.

 

I have heard of dirty / old MAF sensors causing this issue. It may be worth the few bucks to get a can of MAF sensor cleaner and try it out.

I would be inclined to say it's just the starter, but you indicate that it's a rough idle after starting, so it seems like the ECU is trying to get the right mixture of fuel and air.