JE are always going to show on All Bases reporting. That is why you should not be using them for most things.

“We run both accrual and cash P&L’s. A journal entry made to accrue costs also shows on a cash basis P&L.”

That is because you need to use the Bills […]

Resolution for 'Bases reporting issue: 'Can I designate a journal entry to be an accrual basis entry only?' available: Yes.

The Bases reporting 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 Bases reporting issue yourself by looking for a resolution described in the article. If it is a complex Bases reporting issue or you are unable to solve the issue, you may contact us by clicking here or by using other Bases reporting support options.

For more information about resolving issues related to Bases reporting in Quickbooks/QBO or to get support for the issue 'Can I designate a journal entry to be an accrual basis entry only?', click the link below: