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So, for a while, my trunk hadn't been latching well. I'd have to push down in the center to latch it. Today, it just wouldn't stay down at all. I drove it home and started to look at it.

It turns out, the latch assembly wasn't meeting the striker properly. In fact, it was just barely making contact. Even if I pushed down and it started to push the mechanism, there wasn't enough clearance for the hook to latch.

So, I raised the striker as high as it could go. Nothing.
Then, I tightened the blots on the trunk hinge..little contact
Then, I tightened down the rubber tailgate stops...quite a bit more contact.

Now, I can close the trunk if I push down on the left and right sides.

What could have caused such a gap between the latch assembly and striker?

 
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Did you recently have your trunk stuffed with luggage and had to drive with the lid half open and secured with bungie cords?

 
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Nope. I never had anything in the trunk so big. Hmm...is it possible the trunk hinge could get bent? I would think its pretty strong.

Is there any way repeated driving over speed bumps would cause this? No, I don't mean at high speeds, just the standard speed bump, normal speed. I drive over about 12 of them every day.

 
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The only way the hinges are getting bent is if you slam the trunk down really hard on something preventing it from closing all the way or if you tie it down partially open. Just driving on bad roads with the trunk latched will do no harm.

If you have not been in a rear end collision them something is up with the latch mechanism. Remove it completely from the lid and make sure the lid still closes and lines up properly.

 
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Another thought, did your car recently get stuck in the snow/mud and get dragged out by the rear hook?

 
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Thanks. I've taken the latch off (it was the first thing I did) and the trunk closed just the same, there just happens to be a large distance between.

Does anyone have a photo of the latch (in the open position)? I'd like to compare.

 
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put rear seat down and go inside the trunk to see how it looks like. take pics if you can.

 
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No no...I would like to see what a "good" latch looks like so I can compare to mine in the case there is something "broken".

 
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Ok so if I am understanding this correctly, by removing the latch you have verified that there is no alignment issues with the hinges by checking to see that the trunk closes with even panel gaps on all sides?

Is your latch by any chance in the "latched position" and out of sequence with the trunk lid?

Do a Google image search for "civic trunk latch" I found tons of pictures you could compare yours with.

 
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Correct. There is actually a gap on one side. It eventually is closed but still remains uneven. The latch is in the correct position. This is clearly a case where the vertical distance between the striker and latch is far greater than its supposed to be. The adjustments I made seemed far beyond what I was expecting.

 
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Time to start screwing around with the hinges. unbolt the trunk ;id and figure out where you need to add washers so it closes even.

Big question is how did this just happen out of the blue? I'm guessing there was something large in the trunk that one of the hinges got crushed against.

 
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You need to bend the latch. I had the same issues with having to push the trunk down in the middle and all that crap. My trunk was popping open when I went over bumps. I took the covers off the latch mechanism and bent it and and twisited it until I got it right. It is now perfect. Give this a try and let me know if it works.