A problem with the 12v battery can impact the computer, which can make the car act odd. It happened to me. Replace the 12v battery if there is any doubt.

Regarding the software upgrades.... I have a 2006 and the dealer has performed the software upgrades several time at no charge. Having said that you might want to ask what is being upgraded.... it seems clear to me and others ....that the purpose of some of the upgrades may be to mask when the hybrid battery starts to get marginal.

It's a long story but Honda America replaced the hybrid battery after some back and forth even though there were no error codes. I suspect that had the original software not been updated there would have been errors codes.

 

I've had updates twice (at least) and never been charged a dime.

 

Following up on my own post, I called American Honda and they said it should have been covered under the emissions warranty, which in California is 15/150. They emailed the service manager to this effect. I also talked to the service advisor about it who said he would look into it further. He called me a little bit ago to confirm that it was covered and they will be refunding the charge.

 

I can only speak for my update, which was marked as "performed ECM updates for computer on vehicle" on my invoice. YMMV. I really don't know about a diagnostics fee. Also, I'm in California and those states with CA emissions requirements have a much more generous warranty than in other states.

Edit: I forgot to answer one of your questions. No, I had no IMA or CEL lights come on. I was just experiencing general weirdness (not holding a charge, charge level changing spontaneously, forced regen when there were 5 bars) with my IMA battery,

 

OMG. I am so happy to find this thread. I am just about to hit 100k (2007 HCH II) and my IMA battery has been exhibiting these same symptoms for the past month or so. I though I was imagining it, or it was the heat (which does seem to make the problem worse). No light has ever come on but the charge drops (every time I drive); acceleration is sluggish when I lose the bars; I completely lost ALL bars once (which was kind of scary); MPG has dropped noticeably; and even after it recharges it doesn't hold the charge well. Called the dealer this a.m. to set up an app't. They told me the battery for the 2007 HCH has a 10 year/150K warranty in CA - phew (because by the time I drove to the dealer today I would probably be at 100,005). Thank you all!

 

Hondas track record for the 2006+ civic hybrids is to flash the computers so that the IMA light doesn't come on and avoid an immediate replacement of the battery pack. And if you complain they have told the dealers to run "tests" and all of these come up normal, even though we are getting 30mpg, daily recal, and have no power, so again they dont replace the battery pack.
In summary, their current track record stinks. As soon as the service manager responds to me, I will be informing him and Honda of their so called "customer support".

 

Update on my previous post:

Since the software was updated my MPG has been in the low 30s and the battery performance has been worse than ever. The original problem was that it didn't hold a charge overnight. Now the charge status lights seem to be on at random. Since I drive the same hill (Sepulveda Pass) every day to and from work I know where the lights should be at any given point, and they show full charge when it should be discharged and vice-versa. It seems to recalibrate once or twice a day and go into forced regen when at 5 or 6 bars. The IMA seems to never kick in when it used to and I'm regularly hitting 4-5,000 RPMs when accelerating.

Over the weekend I drove to the Bay Area and back via the Grapevine. Coming south over the Grapevine, where I would normally start with 4 or 5 bars, it had 6 bars yet drew no power from the IMA the entire uphill trip. After the car had been parked for 1.5 hours I drove it to dinner and heard a fan in the back seat, which I had never heard before.

I took it to the dealer today. Different service guy than the one who charged me for the software upgrade (still working on a refund) since he no longer works there. The guy said it passed all their tests and that there is indeed a fan back there when the battery gets hot. (He had to call Honda about that because he didn't know there was a fan there either.) So he's saying that there's nothing they (the dealer) can do and that i have to get a paper trail going for Honda to replace the battery.

 

Had mine replaced last Thursday. Car DEFINITELY seems peppier when accelerating and IMA charge indicators seem much more "normal." My mileage, however, has not improved and a 48 mile commute where i used to get 45-48 MPG is still hovering around 39-40 MPG (although this is only commute day #2 after replacement and the weather is beastly hot, for what that's worth).

 

The last two posts are my same experience. I just got my IMA battery replaced, 6 days ago, after two months of arguing with Honda, an online video and threats of trading it into Toyota.
Mine is peppier with more assist but battery drains faster than normal. I still dont get 50 mpg to and from work like I used to, even in the summer. I am getting about 40mpg.
BTW, I have never heard this fan in the back.
I took my Honda in for an oil change in Feburary of this year, which they did computer updates also. I am wondering if this was the beginning of my car problems. It seems to correlate.

 

you could try checking if your fan is running after you get out, I notice it running a extra long time, and starting and turning it off does turn it off, honda has a under size battery,and on a civic a lower battery wouldn't be notice