I need to create a second partition on my SD card to use Link2SD to store apps on it, but every time I make a second partition the phone says there is no SD card at all. I've tried it a few times with FAT32, ext4 and none but the phone always says "no SD card". When I delete the second partition it works fine and I can access all the data I had saved to my SD card.
Make sure you're making the second partition primary. Both partitions need to be primary, just because it's the second one it still is primary.