Due to a problem in the Quartus® II software versions 10.0 and 10.0 SP1, the ALTLVDS_RX megafunction may lose your previous selections when you reopen the megafunction in the MegaWizard™ Plug-In Manager. When you first create an ALTLVDS_RX megafunction, the variation files are created correctly with your selected ports and parameters. However, when you reopen an existing ALTLVDS_RX megafunction for editing, some ports or parameters may revert back to default settings.
To work around this problem, verify that all ports and parameters are set according to your design requirements before generating ALTLVDS_RX variation files from the MegaWizard Plug-In Manager.
This problem is scheduled to be fixed in a future version of the Quartus II software.