Yes, there is a problem with the setting of the input clock frequency in the ALTLVDS_RX and ALTLVDS_TX megafunctions in the Quartus® II software versions 10.1 and 10.1SP1
If the data rate is set to a fractional value then the derived input clock frequency only shows values as an integer.
The PLL summary report will also not show the correct input clock frequency.
A patch is available to fix this problem for the Quartus II software version 10.1. Download and install Patch 0.40 from the appropriate link below.
This problem is fixed in the Quartus II software versions 11.0 and newer.