ATMega128 A/D Floating
You seem to be assuming that the ATmega itself has no influence on the node voltage.

In fact, if you look at the data sheet, the input leakage current is specified as up to a microamp in either direction.

A microamp across 499K is half a volt.

This might or might not be the explanation for the actual issue you see, but it is an example of an invalid design assumption - regardless if this is what is happening or not, it's a situation fully allowed by the data sheet, and therefor a design error to assume that it will not happen.