Once your client finishes downloading the block chain then everything should show as confirmed.

When you first received some coins, especially if they were mined rather than transfered, you cannot go and immediately spend them - for security reasons, you're foced to wait for a number of blocks. Once your coins have appeared in all those blocks then you can indeed go and spend them.

E.g. for Primecoin, should you receive some coins you just mined, you have to wait for 2 days before spending them. If they were transferred to you by someone else, you just have to wait for 3 mins (3 blocks). Likewise with other coins.