I use a Xonar Essence STX (PCI-E 1X) in a PCI-E 16X slot
PCI-E standard specifies that it should work.
If it doesn't, then I'd say it's a motherboard bug or all the PCI-E lanes are already being used by other slots (motherboards have a limited number of PCI-E lanes, and some will split the lanes between slots depending on which slots have devices in them, eg assigning 16 lanes to one slot or 8 lanes each to two slots)