This happens with HDSP cards. RME has a page on it.
Their story is that some of the older HDSP cards require a voltage level that the PSU fails to provide during booting, and if that happens, the card is never visible to the BIOS. They have a h/w hack to work around it, but I think their recommendation is to get a better PSU.
However ... this has happened to me with an HDSP card in a machine in which it had worked for years. I did a kernel upgrade, and after the reboot, the HDSP card was never seen again. I installed it in 3 other machines, and it was not visible there either. This happened years ago (perhaps 4?) and I never got the card working again; I also moved onto computing hardware with no physical space for a PCI card like this.