"Specify input clock rate" for ALTLVDS_RX only allows 100MHz

I I tried with my local installed QII 10.1 and QII 13.1, there is no issue selecting other clock frequency in ALTLVDS_RX. Probably you might want to try re-installing your QII version or try with newer version to see if issue persist?

By the way, just wonder what are your LVDS_RX configuration? Probably the specific configuration only allow input clock frequency of 100MHz.