Isaac-
Which version of the FPGA module are you using? The context help for the timed loop in 8.0 and 8.2 reads "...If you use the Timed Loop in an FPGA VI, the loop executes one subdiagram at the same period as the FPGA clock." If you want a custom loop exeecution time, I recommend using the Loop Timer inside a while or for loop instead.
Xaq