FPGA configuration time and PCIe secification

The Answer - I havent used a cyclone for it, but we did use a stratix 2 GX in this scheme. The result - some boards that wont boot in some motherboards - and it wasnt even a specific manufacturer thing - some boards worked and some didnt.

The larger devices take a long time to program, so will fall outside the PCIe spec. You HAVE to use FPP or you're going to have problems. But Max IIs can do it and are very cheap and very small. The PCIe dev boards all use the FPP scheme if you need a reference design. Theres even a free FPP block you can pull out of the megawizard, so design is pretty small.