Sometimes, a cache-related problem can cause odd behaviours in QuickBooks Online. This is likely preventing the boxes from appearing on the Reconcile page. I'd be glad to help you fix this.
You'll want to isolate this by using a private or incognito window:
Google Chrome: Ctrl + Shift + N
Mozilla Firefox: Ctrl + Shift + P
Safari (new versions): Command + Option + P
From there, log in to your QuickBooks Online company, then go to the Reconcile page. When the boxes appear, go back to the regular browser and clear the cache. Close it all out after doing so to complete the process. Instead of clearing it, you can also use a different supported browser as an alternative.
Do you use the QuickBooks Online Windows app instead? Click the Help menu, then choose Reset App Data.