Check Link2sd settings.
I don't remember whether Link2SD cares about the order of the partitions. For most apps2sd solutions you put fat32 as the first partition an ext as second, so if you put them the other way round that might be a factor. Both partitions should be primary I believe.
Finally, how did you make the ext partition? When I used to have a HTC Desire (very little storage) we saw a lot of people make ext partitions which the phone couldn't use, and they had always used Minitool Partition Wizard to partition the card. People who used GParted never had such problems. So if you can't find anything else but did use Minitool you might try remaking the partition (I don't know whether Minitool has got better, but this was the answer in enough cases that I distrust it).
