Honda Civic Hybrid IMA battery problem?

I recently purchased a 07 Honda Civic Hybrid (with about 48000km on it). The IMA Check Engine light came on when I test drived the car. I asked the sales what the problem is he said they just need to reset the car computer. The light went off, but on the day after I purchased the car the IMA Check Engine light came back on again. Took it back to dealer, they said they had to update the software. The lights are not on anymore now, but mileage is 6.8 liter/100km, as opposed to the 4.9 or so average stated by Honda. I am thinking that there is something wrong with the battery, and that I should be getting a better mileage than what I'm getting now. What can I do about this mileage problem? Is there a problem or is it normal for the mileage to drop after 3 yrs of driving?

@shorty: I've driven the car for about 500km already since they've updated the software, but thanks for letting me know.