Incandescent headlights? Or have you upgraded to halogens?
The headlight switch has a self resetting circuit breaker in it (to the best of my recollection). Headlights that draw much more current than stock (or wiring issues) can make that breaker overheat and cut power. Then it cools and switches back on. It happened on my '71 when I installed 55/60W H4 headlights. I don't recall the on/off rate but it was more than a few seconds each on, then off, then on... The solution is to reduce the load on the switch, put in a headlight relay or kit, use the switch to drive the relay (only) and the relay to power the headlights.
Or maybe try a new headlight switch. The breaker can become more sensitive with age.