Have you checked your alternator to make sure that its supplying your battery the proper voltage? That would be the only thing that i could think of that would cause your car to bog down a little when the lights flash?
Sounds almost like your timing belt slapping or an exhaust leak too. unless you have an aftermarket exhaust. Try putting your hand over the upper timing cover and see if you can feel the belt slapping against the cover. If no luck there, I would check for an exhaust leak.
1. Check alternator output
2. Check timing cover for slapping belt (stretched)
3. Check for exhaust leaks
Could be something related to EGR or something of that nature as well as far as the idleing but that wouldnt account for the loudness and the sound its making.