None the less, you're going from a 3.0.0.4.388 firmware version to a whole new code line of firmware. Not just a change from 3.0.0.4.386.x to 3.0.0.4.388.x, but a change from 3.0.0.4.xxx to 3.0.0.6.xxx. No telling how the settings from the 3.0.0.4 map into that for the 3.0.0.6 firmware. Or how the defaults map over such a major change in firmware.
And yes, it wouldn't surprise me at all if the updates to the Asus Router app would lag such a major change.
Hope this makes sense...these major firmware family changes seldom happen, but when they do, watch out *smile*.