There is a bug in KSP which causes the command seat to turn kerbals into debris. This is a very common problem so I am re-posting my explanation and solution here:
It's true that the command seats cause the kerbals to become debris, as you stated. I have driven rovers many hundreds of kilometers on the Mun and Minmus, and have had this happen many times.
In fact, it seems that just touching the command seat the wrong way can cause this! More than once I've had kerbals standing in the rover collecting science, when the rover starts to roll, causing the kerbal to bump the seat and fall out. Not every time, but sometimes the kerbal becomes completely unresponsive. It seems that the harder he bumps the seat, the more likely the chance of him becoming zombified.
Here's how I revived them a couple of times:
(WARNING! If you don't know what you're doing this most likely is not going to work for you. Back up your quicksave and Persistence files before attempting this!)
1.Stand a fully responsive kerbal beside the zombie kerbal.
2.Quicksave with F5
3.Minimize the game and open the quicksave file with Notepad or any text editor. The quicksave and persistence files are in the Saves folder within your KSP folder. Your KSP folder location depends on whether you're running the Steam or non-Steam version. In any case, it will be somewhere inside of your Program Files (x86) folder if you're running Windows 7. Sorry, I don't know about Linux or Mac.
4.Find the zombified kerbal in the file.
5.Open the quicksave file with Notepad a second time.
6.Find the responsive kerbal.
7.Compare the two and you'll see the lines that declare him as debris. Edit them appropriately according to the "good" kerbal.
8.Save the quicksave file that you edited. Be very careful because Notepad will save it with a ".txt" extension if you don't know what you're doing.
9.Go back into the game and hold down F9 to load the quicksave.
If you've done it correctly, zombie kerbal will be cured. It has taken me more than one try sometimes to be successful, but it works.