I have had this problem, and it seems to be a problem with the machine you use or the import process. I was traveling with an EX3 recently using my Macbook Pro to offload and then import clips in FCP. Occasionally I would get the same blocky green/black lines you’re describing. It doesn’t seem to be a “dropout” or anything wrong with the original media on the card, because the clips would always play back fine in camera or in Clip Browser directly from the card, and when I tried transferring the same media on a different Macbook I didn’t always get the problem in the same areas. The corruption seems to be introduced by the machine or the software at some point.
At the time I experienced this, I was doing what you did and fixing it by re-importing the problem areas, which usually did the trick, although sometime it seemed like I would have to reboot first, sometimes multiple times. Since then I’ve imported a lot of media using several other machines (mostly Mac Pro towers) and never seen it again. So the issue seemed to be with the Macbook Pro, which I recently did a complete reinstall on (for various reasons, this being one of them) and haven’t had a chance to test again yet, but I’m curious to see what happens.
So the good news is that your footage is all probably fine, you just might have to jump through hoops to get it imported properly on some machines it seems.