but again I couldn't tell which of the ingredients was the problem child, or whether it was because I had microwaved them.

It's because you microwaved them. It tends to make the eggs rubbery, and doesn't give the herbage time to develop a flavor characteristic in the eggs. So you end up with rubbery egg with green stuff.

Try soaking the herbs in 2 TBLS of milk for at least 20 minutes before cooking to rehydrate them and "bloom" the flavor. Then mix in with the eggs and pepper (Salt should be added afterwards).

See if that helps.