Frenzies I have the same and it worries me. You can almost peek inside, thats how long some pads go. On the raised pads they're still sticking out a bit even when pushed down. Doesn't it worry or bother you?
After time and a lot of finger drumming they could disappear completely and will be absorbed by the DSP. I am going to swap mine for one where all pads are neatly raised.
I'm not sure about the batch number but the serial was somewhere in the 9500's. Can't check anymore as it's boxed up and ready to go. Hopefully I can get a new "raised pads" unit tomorrow. It
looks much better when the pads are all the same height, and will also play better due to better travel.
It does seem very common when Google image searching, but I see just as many with all pads raised nicely. I would assume Korg meant to raise the pads above the frame so somewhere during assembly something got skewed. Should be an easy fix, if it wouldn't void the warranty it would be disassembled right now.
Also I read on the Gearslutz forums that some people had to "bend" their E2 cuz it was wobbly. I wouldn't try that though.