"If my memory serves me well, Xilinx actually have an application note"

Is this the one you're thinking of:
"Quadrature Phase Decoder in XC3000 FPGAs" http://www.xilinx.com/xapp/xapp012.pdf

In the Introduction, this sounds like the problem Erik is describing:
"A common technique for counting objects is to pass them through a light beam. Problems can arise, however, if a part dithers on the edge of the light beam and is
counted more than once, or if the direction of motion changes and a part is recounted rather than uncounted."

A State Machine is presented to overcome the problem.