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My vote is with the tune. Tuning is great and can really allow these cars to tap into all that unharnessed power but when you start tuning your playing with the manufacturers specs and headaches start to occur. I would check the plugs, the coil packs, and the connections. Heating and cooling causes things to expand and contract and something could be funky/out of spec when she heats up. You could also try cleaning the Mass Airflow Sensor (MAF) typically found on the intake jutting out the side. I had a 2008 335i that has something similar happen and it ended up being a faulty MAF causing things to get all out of whack. Sounds like something at temp is causing either something in the ignition or ratios to be out of whack.
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