What is the difference between the paydays?
There are two different values for payday when you hold tab during a mission:
As you can see in the image, the payday on the bottom-left is about $500 000 less than the payday on the top-right.
What is the difference in meaning between the two?
Solution 1:
The value at the top right should display the correct total value for the payday, and I'm pretty sure it increases as you pick up instant cash and secure bags. I imagine the total at the bottom left is summarising how much you have gained from the bags you have secured.
Solution 2:
As you progress through a mission you get instant cash, bonuses for finishing the mission a certain way (stealth vs loud), objectives completed, and bag items contribute towards the end result.
If you secured the bags it is probably why the number went up.