Blinkers not working

A few months ago my right side turn signal stopped working properly. When I would activate them they would flash once or twice and stop all together, if I turn the key to stop power to the system it will reset it for another two flashes. I replaced the turn signal switch on the dash with no improvement. I removed the relay/fuse box under the hood and checked the connections, they all looked fine so I put it back in place. Upon doing so my turn signals worked like new but my check engine light was now on. Yesterday while driving I used my right side signal and my check engine light turned off and my blinker stopped working again. Any ideas on what is happening would be grateful. I have isolated the problem somewhere in the front right but all the wires/connectors have been checked and cleaned to ensure good contact.