How do I print a cheque that has been marked paid. There isn't an option at the bottom saying Print Check because the system thinks it's been printed.

Glad to have you here in the Community, @jluwiera. 

I've checked my tools here if there are reported issues about the missing Print Check button when printing a cheque. But currently, there aren't any. 

Accessing your QuickBooks Online (QBO) account using a private browser is a good way to start isolating this issue. This way, we’ll know if this is caused by overloaded data in your browser.

Here are different keyboard shortcuts to open a private browser:

• Internet Explorer: Ctrl + Shift + P
• Safari: Command + Option + P
• Google Chrome: Ctrl + Shift + N
• Mozilla Firefox: Ctrl + Shift + P

If it works fine, go back to your regular browser and clear its cache. The cache is stored in the browser to speed up its performance, but too much can accumulate and slow down its processes. For the detailed steps, you can go through this link: How Do I Clear My Browser Cache and Temporary Internet Files?. 

But if you're unable to print a cheque, I suggest using another supported browser.

Once done, you'll have the Print or Preview option at the bottom of the Cheque screen (see the screenshot below). For more information about this, you can visit this article: How To Print Cheques. 

If you need anything else, I'll be keeping an eye out to your response. Have a great day!