Are you absolutely sure they are not producing any more eggs? You could just be having bad luck with the random number generator.
Every 256 steps the game will decide if an egg is produced. The chance of there being an egg is less if the Pokemon like each other less. If the daycare man says "They prefer to play with other Pokemon" then they are incompatible but I'm sure you know that.
His message will not change for the same two Pokemon. Make sure you didn't also take one of the Pokemon out or replace it with a different one that is not incompatible.