Well I don't entirely agree with some comments here :
Malaysia Airlines and Singapore Airlines are two carriers that have won excellent accolade throughout the world over the years.
The fundamental operating and service differences stem from the split of Malaysia-Singapore Airlines. Whilst some say that MSA should never have split - it is obvious that Malaysia, Brunei and Singapore could never cope with one airline servicing the three nations - although Gulf Air doesn't subscribe to this (NB. The Gulf nations are very much smaller).
Malaysia Airlines (MAS) was set up to operate domestic and a selected few regional flights based at Kuala Lumpur, whilst Singapore Airlines was set up as the International division (hence S.I.A). This led to MAS being run as a public service company - much like a national railway or bus company. SIA meanwhile was groomed to fly to exotic and faraway cities and with this came international exposure.
This is the main reason why SIA tends to have a higher profile worldwide whilst MAS has found itself chasing after SIA in the international arena. Service fundamentals don't really vary too much between the two carriers (numerous discussions have been had on this forum in the past) but you can't escape the fact that more international travellers recognise SIA more that MAS dur to the above history.
On the operations front - SIA still does not have a domestic division which many carriers would confirm can drain an airline financially - especially with the low government-set airfares in Malaysia.
So all in all - both airlines deserve to win awards. There is little politics involved with the running of either carrier - it is just the fact that although they are neighbouring and competing airlines, they operate in rather different markets.