The problem is with the range you selected for the Conditional Formatting. You selected the entire column for Column AE which then applies the formatting for the first Row 3 Comparison to the cell(s) in Row 1 since that is the first row of the selection.

As I stated earlier your selection to apply the formatting MUST begin in Row 3 to match the formula. Also, the formatting is only applied to random cells in Column AQ so you will not get accurate results there either.
That is why AE1 and AQ1 are formatted because the first comparison which is in in Row 3 is TRUE so it formatted the first row of the range which is Row 1.
The easiest way to fix this is probably to start over.
- Delete the current rule.
2 Select AE3:AE?? (I can't see how far down your data goes--thus the question marks). If you also want Column AQ to be formatted, use the Control key to add a range. With control held down select AQ3:AQ?? (Use the same end row in the range as you did for Column AE).
- With those ranges selected, go to Conditional Formatting>New Rule>Use a Formula and enter the formula as you had it.
=$AE3=$AQ3
That will apply the formatting to the correct row where the data actually is.