A blinker relay uses a thermal switch which is a piece of curved, spring steel and a thinner piece of spring steel near it that has a wire coiled around it with a resistive property.
When current is applied to the relay the coil of wire heats up and expands the small piece of spring steel until it pushes it to make contact with the larger piece of spring steel. All of the current then travels directly between the two pieces of spring steel. Since no current is flowing through the coil of wire any more, (electricity always takes the path of less resistance), the small piece of spring steel begins to cool down.
Once sufficiently cool, the small piece contracts and pulls away from the larger piece and breaks contact. Current again begins to flow through the coiled wire and begins the cycle again, causing the light to blink.
No matter how precise the relays are manufactured, there are far too many variables for any two relays to blink at the same rate. The resistance in the wire can be slightly different. The temperature of the relays could be different, perhaps because one car has the A/C on. Many different materials could be used by different manufacturers. There are many reasons for slight differences.
Any slight difference between the two relays will end up heating and cooling at different rates. Meaning they will always blink at a different frequency.
For a fairly simple explanation look on How Stuff Works.
