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I had this problem with my truck a while back. I replaced the headlight switch and it was all better. the old one had a short i think (it had actually gotten hot enough it had melted).
While you are in there put a high beam and low beam relay in that takes the current out of the switch... I will look for a write up. I have done this on other vehicles and it makes a huge difference on brightness (better amperage to the bulbs)
I went through 3 headlight switches. After a while the blinking would come back. I changed the bulbs, it still came back. I traced out the wiring looking for a short and found nothing.
I then put in a relay and I haven't had a problem in the 3 years since.
Next time the lights start blinking flash the high beams on and off a few times. If it goes away then I'd think it was the turn signal/high beam stalk. I had a problem with mine where the headlights simply wouldn't come on at times. I replaced the light switch but the problem did not go away. I finally realized that flashing the highs on and off would get then lights to work. When even this didn't work I replaced the stalk and all was good. When I opened up the stalk you could see where it was burned from making a poor connection. I would think that headlights flashing could also be caused by a problem in there. I bought a cheap replacement off ebay but the turn signal canceling thingy broke fairly soon after. Fortunately I kept the old one and was able to swap the plastic part from the old one into the new one and it's been working great ever since. I'd guess it's been over a year now. I think I paid $35 if I remember right.
Look at the plug on the head light switch real close, you are looking for a burnt wire, or plastic will probably show some sign of heat damage. also look at the terminals on the switch for any discoloring. if you see any of this replace the connector and the switch. I think this has been the problem for every flashing headlight problem I have ever fixed.
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