So you didn't replace the flasher with one designed for LED's? The stock ones are designed for regular bulbs. The current used by regular bulbs is what triggers the flasher unit. With LED's, the current is not drawn near as much as regular bulbs. When the flasher is flashing so rapidly, it will burn out faster.
My bet is that the flasher unit is fubar'd. Replace it and all should be good. Replace it with an electronic flasher or one designed for LED's. If you can't get one, then put a resistor on each side of the vehicle. They can be found around the internet for fairly cheap. This will make the lights flash properly using the stock style flasher.