Why did my toasted acorn squash seeds smell like chocolate?
The difference between carmelization and the Malliard Reaction

When cooking seeds and nuts, you are essentially carmelizing various basic sugars and amino acids (the components of protiens) via the malliard reaction.  This is what gives a grilled steak a different flavor than a boiled one, just like white table sugar has a different flavor from carmelized sugar via carmelization.

When cooking anything you are trying to add flavor to, there is a point where it goes from tasty to not-tasty.  Think of a charred steak or burnt caramel.  Some items that we expect a certain amount of bitterness from (coffee, chocolate, etc) are pleasant to smell because they smell like they will taste; a little bitter and likely robust.

When you are expecting a buttery, nutty taste, the smell of chocolate or coffee may seem pleasant, but it tends to signify the seeds have cooked to that doness, which is probably not an ideal one for that item.  A medium-well tuna steak may smell nice, but (arguably) won't taste as nice as a rare/medium-rare steak.

You essentially burnt your seeds. (no snickering!)

I would recommend in the future you pull them out of the oven a few minutes before they smell like you want them to.  They will keep cooking on or off the pan for a couple minutes due to residual heat.