I'm taking a stab in the dark here...

You are staying at Misool, and your flight out is on Express Air?

Express Air is the 'safest' method in that it flies more often than not. Merpati and Lion Air both leave a lot to be desired, especially where connections come into play.

If it was crucial that you made Jogja the same day, I would reverse the flight to Jakarta, and connect to Jogja from there on Garuda. Yes, it seems bizarre to overfly where you want to go, and then come back, but with 9 flights a day you are fairly secure with Garuda in the event of delays. And they are the [U]only[U] Indonesian airline I would risk connecting to an International flight (and they are far from perfect!).

The Merpati and Lion Air flight I believe are connecting somewhere (Makassar? Manado? Both) from Sorong. Not sure if Lion Air 'guarantees' connections? However I will not touch them with yours... And I have had a Merpati flight delayed by 3 days before, so there you go.

Just a brief thought - if you havn't already booked - can you use Silk Air from Solo to connect via Singapore instead of flying back to Jakarta?

GA still have a UK Call Centre - do they have one where you are based?