So I figured it out although I can't understand why it works this way.  So on May 5, there was a balance on the card of $604.25.  I made a purchase on that day of $83.94 budgeted for in Category A.  It comes in the next day and is the wrong item so I shipped it back.  I got an email a couple days later stating a refund amount of $67.15, return shipping and restocking fee deducted.  I changed budgeted amount to $16.79 leaving the category in the red and therefore the credit card showing overspent by the refund amount.  I'm good with this.  Between the 11th and the 14th I made 6 more budgeted purchases on the card from other categories.  CC is still overspent by $67.15.  On the 16th, the refund hit the card.  I categorized it back to Category A which puts it at zero and the credit card available payment=cc balance.  Great!  Until....

On the 17th, I made a purchase out of checking account for $76.43 from Category A.  Available is at zero but this purchase was for someone else so I don't cover the overspending.  On the 18th I made a purchase for $127 out of checking from a different category, also an overspend.  So apparently both of these purchases affected the credit card available amount but I didn't realize it.  So today I look at my budget and notice that the payment available for credit card has gone down and it's overspent by $72.13.  I'm baffled which leads to my original post.  I cover the $127 overspend and what happens?  Credit card available changes and I'm now only overspent by $16.79.  How is this possible when the $127 charge was from my checking account?!  Right now, Category A is budgeted $16.79, activity $93.22 and available negative $76.43 (spent from checking).  If I budget that amount to the category, everything balances.  I don't, however, understand why purchases I made from my checking account are affecting the available payment amount of the credit card.