Does it?

[DEB8]

You say they are basically the same. So it appears that they are not exactly the same. Hence a difference appears to have occurred...

[ NB : Loyalty will not change unless a unit general has a different ( Higher ? ) Dread rating. ]

You should note that some provinces have very low income. Any "change" to one of these can therefore be rather small.
You should also note that some Vices and Virtues applicable to Generals reduce a provinces income ( by between approx. 5-20% each ). Perhaps you chose a new one with poor / bad Vices and Virtues...