Hi charlier,
Not sure if this will work the dates you are travelling, but after some very determined research, I flew Maumere-Makassar-Manado directly last summer. MZ 7065 and JT 740 (Merpati and Lion Air) were the flights.
The Indonesian travel agency associated with my Alor liveaboard had insisted the only option was to fly Maumere-Bali, then overnight, then fly Bali-Makassar-Manado which would have wasted significant time and money for me since I was heading to Lembeh. I did not believe this was the only possible way, given that Makassar is such a major hub. So I started by googling all the airlines that flew out of Maumere, then checked each airline's website individually for Maumere-Makassar flights. While the meta-search engines are good, I am finding they still don't capture all the flights (I have been working on other domestic tickets for this summer). Once I found the flights, it was no trouble to book them through any agency.
My original routing was supposed to involve a 10 hr layover in the very nice Makassar airport, but that was still a lot shorter than most of two days to fly to Bali then all the way back to Manado. I was travelling on a Sun. In the end, my flight out of MOF was moved earlier 4 hours at the last minute, which made it possible for me to catch an earlier flight and have only a 1.5 hour connection (I chose to cancel my original Makassar-Manado ticket).
Edited to add: of course if you are flying SIN-DPS it may be easier for you to fly out of DPS, rather than open jaw MDC-SIN. The Silk MDC-SIN flight only leaves midday, so I guess you would have to overnight in MDC if you flew this route.
May not help you, but just in case.
i can't do different...:depressed: one is bali-alor via kupang and the other is alor-maumere via kupang... 
