Don't worry, you're not going crazy and neither is NinjaTrader. You just have a different workspace open with those charts in it.
You can switch to that workspace by navigating to the following from the NinjaTrader Control Center: File > Workspaces > [Workspace name], then close the workspace by clicking File > Workspaces > Close Workspace.
Make sure when you are done using NinjaTrader for the day, that you close every workspace you have open except the blank one. When you close NinjaTrader, only the blank workspace should be open and nothing else. If the blank workspace is not open, then open it, and close the rest of them.