The <4x PCI-e slot was a suspected issue for a long time but no one had actually verified it to my knowledge.  I've only ever mined on 4x or greater slots.  The transfer speed is only 500MB/s per lane with PCI-e 2.0, so it's possible that using only a single lane may cause a bottleneck.

You can verify this simply by moving around the cards.  If the same cards are fine in an x16 slot but awful in an x1 slot, then you probably need the extra bandwidth.