Could you describe the case in detail?
I used LEC alot. It should be equal for A--INV--DFF--INV--B, and A--DFF--B. LEC check what is called key points. ie prime input, prime output, latch, register, hardblock.
So in your case, it will definitely pass. Didyou compare the RTL and GTL? Just try a simple case of IN---DFF---OUT in RTL. You will get IN--DFF--BUF--OUT by add setting BUF the driving cell. If it could not pass. Check your LEC script. In fact, you could just use the sample script from LEC and change the RTL list and GTL file name. And set the hard block list in the script. It will work.