If it's intermittent that's not unusual, it will probably get worse pretty quickly.
I assume you have bolt down coilpacks which don't fail that often at all. The amp in the side of the airbox however is a likely candidate.
I reckon the place that did your flash the other week will be able to scan the ECU for you.
For a possible free fix, have a look at the sparkplugs.
Gavin
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