I really don't know how Vettel's KERS system worked at malaysia but Webbers didn't. It seems a bit strange.. and even though Vettel's was working, he was told by is team not to use it for the majority of the race which i dont see the point in if they are carryig all that extra weight.
There are several reasons to do this. Just off the top of my head it could be:
1: Mechanical failure, causing a performance degradation. Wouldn't want that to happen to the leading car.
2: Electrical connection or wire short failure: Could easily cause a fire, throwing away points.
3: Whatever failure they've been trying to track down has been destroying the evidence when it lets go. In this case you stop using it as soon as the first sign of trouble shows hoping you can find some evidence.
Case 3 used to be very common with engines, particularly with oiling problems. If you were out of the points anyway you'd pull the cars in before they blew.
If it were case 2 and I were running the team, I'd be tempted to bring Vettel in for a cautionary stop, even if it meant giving away 1st.
On the other hand, if they really did separate Webbers car from the others that pretty much screams electrical problem, so....
You can't say RB are 2 years behind. I doubt anybody seriously put development time/money into kers last year. You need to remember that DURING last year kers was dead, and seemed very unlikely to return. Also, it is the nature of engineering that once somebody else has found a solution to a problem, even without any knowledge of how they solved it, you can solve said problem in much less time. RB are, worst case, 3 months behind.
When F1 switched from V-10's to V-8's several teams had problems with components that had been well established and reliable for years. Some of the old timers chuckled and commented that the young guys were going to have to learn how to live with a V-8. The current cars are extraordinarily hard on parts, particularly electrical connections and wires. It's been said more than once that if a wire on a current F1 car can move at all that it WILL wear through the insulation during a race.
Renault may be 3rd in kers development, but they still abandoned it for a big chunk of '09 and can be assumed to be well behind the big 2. I wouldn't be surprised of they were behind Mercedes as well.
If we assume for the moment that the RB representatives are being honest, all of their kers problems to date make perfect sense. They all apear to be teething troubles with a new system, complicated by the teams decision to push the packaging limits and complicated further by massive restrictions on testing.
There's no reason to go chasing conspiracy theories when you can find a perfectly rational explanation from given statements. The only thing I'd add to those statements is a sentiment that's been put forward by several others here, which is that kers still seems to be very much a marginal tech. I wouldn't be surprised at all if they pull it off for the next couple of races. A malfunctioning kers could easily put you out of a race, whereas running without kers may not have any negative effects at all, and at worst will drop you 1 spot at the start.