JUST HERE BECAUSE MISERY LOVES COMPANY!!!
Experiencing the exact same issue and problem...Have spent probably 4 or 5 hours speaking with multiple support agents - verifying setting, explaining the issue, etc. etc. etc. IT's been a clinic in frustration and lousy customer support.

The worse part is instead of acknowledging that it's broken I've been told MULTIPLE times, and as recent as today by a "supervisor" that it's working "as designed" and it will work this way moving forward and I have two choices.
1) Fund Payroll from Quickbooks checking (WHICH I HAVE NO DESIRE TO DO)

or 

2) Use Journal entries to correct the inaccurate entries made to the QuickBooks Checking Chart of Accounts.

BOTH OF THESE ARE UNEXCUSABLY WEAK SOLUTIONS AND QBO SHOULD BE EMBARRASSED TO EVEN SUGGEST THEM.

I've even attempted to close my QuickBooks Checking account as a work around since it's been nothing but problematic anyway.  However, QBO will not allow you to set it to inactive so it does no good.