DDR2 HPCII v11.0 problem, thanks for help !

Failed in simulation or hardware?

I would offer two things then:

1) If it fails in hardware -> check pinout.

2) Raise a Service Request and send them your archived project (.qar)

Also have a look at example projects of development kits. For example:

http://www.terasic.com.tw/cgi-bin/page/archive.pl?language=english&categoryno=142&no=513

or

http://www.terasic.com.tw/cgi-bin/page/archive.pl?language=english&categoryno=39&no=260

I think Arria II or Stratix III are old enough to have project examples with ALTMEMPHY.

Are you using full rate bridge or half rate bridge?