There can be problems with the Spartan-6 FPGA phase detector control signals in some situations. There is a simple workaround that is described in this article that will be published in the next version of the User's Guide.
Solution
To ensure proper operation of phase detector the INC signals to the delays should only be asserted high simultaneously with the CE signals and should kept low at all other times when in phase detector mode. Refer to figure 3-4 in the Spartan-6 FPGA SelectIO User's Guide.