LTC6957-3 voltage level drop in clock input

Design Note 514 has a detailed description of this circuit. http://www.analog.com/media/en/reference-design-documentation/design-notes/dn514f.pdf 

The goal of this circuit is to increase the slew rate of the input signal to avoid amplitude noise to phase noise conversion.  The diode in the circuit will clip the amplitude, which is what you are seeing.  The LTC6957 has has some internal diodes that clip the input signal.  This is ok, as long as the slew rate increases.