I have also a June 30, 2015 Ertiga and also got my license plate after ayear, and actually pareho tayo ng problema.
Luckily for me it was found out by my insurance broker, when I have to renew my TPL.
They alerted me that my license plate documentation is not yet submitted to LTO, and told to me ask my casa seller to submit to LTO all the necessary documentation, at nagawa naman agad ito ng casa Shaw.
I found out also na yung mga vehicle na galing sa 3 years registration ay hindi na kailangan ang emission test, kaya naging madali ang renewal ko.
I hope this will help you.

personally, i'd register it on my EP's designated month, before the 3-year registration lapses....
1st LTO renewal after 3 yr registration