This appears to be part of a larger problem. For instance with my Asus Rampage II Extreme I experience waking up from sleep problems when the Xonar Phoebus is installed on any PCIe x1. I managed to solve the problem 100% by configuring the last slot to x8 (actually runs in x1 width).
To elaborate, the PCIe auto config with two GPUs installed by default is x16 x16 x1. I must run it in x16 x8 x8 for the Phoebus to not cause waking up from sleep problems. If I'm assuming correctly it appears the card doesn't like running on a x1 slot that's configured by the south bridge.