QB Issue Resolution:

Next time you do and invoice, uncheck the boxes, click save and new and see if the setting sticks for you.  You may have to do it a few times for it to remember.  Always click save and new.

Resolution for Issue 'Recently the online payment checkboxes are automatically checked. Before it wasn’t and now I have to uncheck them every time for every invoice.' available: Yes (Solved).
Source: Intuit Community forum.

Recently the online payment checkboxes are automatically checked. Before it wasn’t and now I have to uncheck them every time for every invoice.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Always click save
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