Make sure you've equipped your deck. Just like any other piece of jewelry or clothing, you need to have your deck equipped to use it.
To equip your deck, open your inventory screen by pressing B (for Backpack) - navigate to the deck by clicking on the tab at the top with the deck. Make sure the deck you want to use has a closed hand icon to the left of it, indicating that is the deck you have equipped. If it does not, you can either select it and click the hand icon at the bottom, or double click it.
You can cycle through your decks when you are not in a duel by pressing CTRL-K.
The same thing happened to me a long time ago. It first started with my friend and then after a week or so it happened to me. I only saw the wand spells and the amulet spells and pet spells. I had a equipped the deck and it still had no spells. I put the spells I wanted in my deck too, but it didn't help. Until finally, I didn't fight at all and they were all back.
