Using an OBUFTDS causes the register to be duplicated, and the equivalency checking might fail.
Conformal does not merge these registers automatically. The registers being merged are inverted and also the outputs of the flops feedback to the input to hold when CE is low.
To work around this issue, add the following to the conformal command line:
add instance equivalencies <inst_name> -invert <inst_name>/N -rev
To find the instance name <inst_name>, you will have to parse through the equivalency netlist written out by NetGen to find the instance names of the X_FF. This is a problem only in the post-MAP and post Place and Route equivalency netlist.
Future releases of Conformal might support this automatically.