It has nothing to do with the capital as such actually. It's just about how much land is contiguous to the part that touches Ming.
Edit: Here is game start as Brunei - a non-tributary country with its capital non-contiguous with Ming:
I then send Brunei's famous ninjas to conquer Dai Viet, Lan Xang and Ayutthaya and mandate loss from non-tributaries increases:
I then annex more of south east asia but leave a blocking Ligor in the way:
No change to mandate loss. I then integrate Ligor:
And more mandate loss. I then moved my capital to Johor and nothing changed. I then moved my capital to Manila itself and again nothing changed. Therefore, it has nothing to do with the capital and is only to do with how much contiguous non-tributary land borders Ming. In the OPs case the amount of land was simply too small to make a noticeable difference to mandate.