I found one strange case that netgen reports ports matched, but in the port list, my AVDD pin is missing, although it showed up in both .spice and lvs.v has AVDD...

This has several possibilities: (1) There was a bug in netgen with respect to pin matching that got resolved recently (a couple of weeks ago), so make sure you have a recent version of netgen; (2) Netgen will match a missing pin to an unconnected pin; this is fairly common behavior with the wrapper cell because magic will optimize out unconnected pins, but they will remain in the schematic- or verilog-side netlist.

Oops, I think I misread the results. so.. False alert! Thanks for the explanation!

It may say "(no pin)" on one side of the side-by-side pin list, but if it doesn't say "failed pin matching" at the bottom, then it's okay.