It will flash the light at a predetermined level of engine knock (or detonation) as it's called. Not sure how much you know about knock etc. but it's basically a measure of if the fuel and air is combusting as it should do. Any abnormal combustion events will cause knock (in very simple terms before anyone tries to get all techie with me

). Knock can be caused by a number of things but the most obvious are too much ignition advance in the ECU, a bad batch of fuel or running on an inferior fuel to that which it was mapped with i.e. running normal 95RON unleaded in a car that has been mapped for super unleaded.
The light flashing is a safety feature to let you know that a certain amount of engine knock has been detected and that the car is not running at it's optimum performance level. Depending upon what level the light has been set to come on at will depend upon how serious an issue it is. Generally speaking, the levels are set low and are well before any engine damage or anything like that would be caused however if the person who has remapped the ECU doesn't fully understand things or has setup certain parameters or tables incorrectly then the 'knock' could well be causing problems.
Hence my advice to get the ECU settings checked by someone who knows what they're doing.
Andy