@Arlingtonctk 

"I'm at a loss as to why it's not matching. I can only get it to match if I run the P&L from the beginning of the year till the last day of the month and the balance sheet set at the last day of the month. I used to be able to run it the P&L from say March 1st to March 31st and the Balance sheet to March 31st and the net income would match."

The net income on your balance sheet should match the net income for your fiscal year YTD.  It should never match just a month unless that month is the first month of your fiscal year.  The way you describe it, it is working correctly now.