About 10 years ago, one of my staff went through a similar experience where his EP application was rejected - and even the subsequent appeal was rejected too. This decision seemed unusual because his immediately previous job was under and EP in Singapore before.
Rather than write a second appeal letter, the office manager and I went down to Immigration and VERY politely asked if they could give a reason why his EP had been rejected because, as far as we could see, every thing was in order.
The way I put it was that, although they had every right to reject an EP without giving a reason, it would be helpful to me to have more guidelines so that I would be able to handle any other foreign recruitments more smoothly.
The officer that we met turned out to be very helpful and agreed that, from what he could see, there was no reason to reject the EP application. He explained that about once a week a vetting commitee meets up to decide upon EP applications and he would be on the next one, the following week. he said that he didn't think there would be any problems. Sure enough, 10 days later, my staff got his EP.
Yes, it would appear that decisions about granting EPs are really as arbitary as that.
The moral of the story: if, as far as you can see, all your paperwork is in order, try going down to Immigration with your new employer and asking VERY POLITELY if there was anything missing from your application. It's probably better if your employer does all the talking. The approcah to take will be that your empoyer simply wants to smoothen the EP application process so that his company can hire and put foreigners to work more efficiently.