I've been fiddling with risers as well, and as far as I can tell it's more a motherboard problem.

For example on ASUS motherboards they very rarely like the 30cm risers, but can usually handle the 15cm risers.  However the exact same 30cm riser and card on an MSI motherboard works perfectly fine.  I have an older ASUS P5Q-E motherboard with 5 slots, and only two of them like the 15cm risers, the rest refuse to work.  There are three on-board x16 slots, and all three can run a card no problem, so it's not the card or the motherboard directly.

I've tried risers in all configurations - completely unpowered (and no cap), unpowered (with cap) (as in the molex is there, just unused), powered (molex attached) and cut (molex attached).  Doesn't seem to make a difference to this motherboard.

I suspect the BIOS and/or motherboards have different thresholds for detecting the cards, and since risers drastically increase the line length you have slightly different timings.  If the BIOS/mobo isn't versatile enough to handle that it just won't detect the card, or it may work flakey.

Other people have mentioned that if your BIOS has settings to force the PCIe slots to v1.0 or v2.0 mode then risers tend to work more reliably, however my BIOSes don't seem to have that option.