EDIT: I've re-posted the proper code, and made my problem more clear. (I hope) At least now people will be looking at the right thing and not guessing at what they think my true problem is.
Zones extends a JPanel, which is added to a JFrame called Dorothy. When done this way, Zones doesn't work as planned. When I declare it as it's own class (public class Zones extends JFrame) and override it's paint function, it works the way I want. Details below.
What it should be doing:
1. Show user the sequence
2. Allow user to click squares
3. if right, Go to 1.
4. if wrong, show reset button that Goes to 1 on click.
What it does when inside another container:
1. Freeze as the splash screen is hidden, and it is set to visible.
2. unfreezes, allowing the player to interact (no sequence shown)
3. Allow user to click squares
4. if right, Freeze (no sequence shown), go to 2.
5. if wrong, show reset button. When clicked, freezes. Go to 2.
The user needs to see what Simon says to play.
Apologies for not providing the code in the post, I was forced to provide a file because I reached the "10000" character limit, despite what Office and 2 online character counters said. (Said I had 9655