I had the same thing happen to my '04 4Runner Sport with just over 81,000 miles on it.

At first my driver side signal was running fast for a day and the passenger side was fine. The next day it was reversed. On the third day both the drivers and passenger's side turn signals were not working. I replaced both of the bulbs (unlike your Runner mine has DRL), however it did not correct the problem.

I also noticed when I removed the old bulbs the filaments were still intact, however the base of the bulb looked like it was shorted out and burnt.

I called a toyota dealer and talked to a service technician, told him what happened, he seemed to think it was an electrical problem rather than a flasher/relay problem.

I took it a local toyota repair shop and brought the old bulbs with me. Though they didn't have an answer for me when I brought it in, after they diagnosed the problem they said it was the actual turn signal/drl sockets were bad. They replaced the sockets and new bulbs (not sure if the replaced ones blew again) and everything was working fine.

Total cost was about $85.00