Exactly. You're lucky to get that old S3 card to work together with another card at all.
Tech background: In general, old display cards can't disable their VGA compatibility function - and since only one card, the primary, may have that enabled, you'll get a clash if you attempt to make one of those old cards the secondary. On top of that, early S3 PCI VGA chips have a PCI bug that effectively prevents them from getting their resources mapped properly in certain newer systems.