Link2SD does not select second partition
According Link2SD page, also the second partition should be primary:


  You should have two partitions on SD card and both should be primary.
  The first FAT partition is your standard SD card storage. The second partition is used for application files and can be ext2, ext3, ext4 or FAT32.


Check if the second partition (the first one can not be used to link apps) is primary and not an extended partition.