Had a couple of instances lately with rough running just after start up with the eml and emission lights on and the engine revving itself up and down. Switch off for a few minutes and it was fine although the emission light took a fair while to switch off.
It could be a lambda sensor playing up. The EML should go out after three 'healthy' starts. Check for error codes with an OBD II reader and you should have your answer
As Beedub says - coil packs breaking down are common. Symptoms sound similar to mine from a year back which turned out being 2 packs that had given up.
Code was P1417,and I have to admit the way I shunt vehicles around doesnt help-start/stop from cold with richening valve constant does the car no favours,will have to get in the habit of letting it run a while before stopping engine.
Another forum member had the code P1417 = "Port Air Relief Circuit Malfunction" and was diagnosed as
" ....it's a split hose. Apparently it's connected to the hot film air mass meter - see picture. Tried looking for this part online but only US sites seem to sell it. Can't be hard to get one and it's only a few hose clamps to undo to fit one".
Actually Ewazix, the P1417 error code was my car a couple of summers ago and the split hose was someone else with a 2.5l and no error code Mine resolved with no treatment.
I did have a further episode of the above when I had a tiny pre-cat exhaust blow due to corrosion between the pipes and the cat heat shield (which had come loose). This time the car had got really hot on a track day and on starting it was running roughly and hunting. This cleared with a restart but left this error code and an audible blow. It was all cured easily with a little welding... The code was due to the pre- and post-cat lambda sensors disagreeing with each other due to the holed exhaust between the two. I'd check the lambda sensors. The other guy on the thread from 2010 had a whistle from the MAF so have a listen there too.
I'll be interested to hear what the final diagnosis turns out to be.