Are you really sure it’s just not interrupting? It seems to me that many conditions could result in a card not appearing to send anything, including many situations where the interrupt lines are perfectly fine.
Electrically speaking, apparently the interrupt lines on PCI are open-drain, while the others are push-pull. I suppose that in theory this could create some difference in behavior between the types of lines.
I can’t imagine that the difference — if it even exists — has anything to do with the physical position of the lines in the connector, especially in regard to contamination. The airflow patterns in every computer are different, and in fact will be individually influenced by the expansion cards installed. So I would expect contamination-based problems to be highly model-specific.
The only possible effect I could see with respect to pin position is that the interrupt lines are practically at the end of the connector (closest to the rear panel, as it happens), and maaaaaybe this affects the angle of the connector as it seats, making it either not seat fully, or to have differences in the wiping action of the contact springs on the contact fingers.