1) The chances of a US airport X-ray machine hurting a laptop are extremely slim, especially if the laptop is completely powered down. The chances of any X-ray machine causing files to be moved or renamed is zero. Those sorts of problems are caused by humans and malicious software.

2) I understand that the TSA does not permit hand-checking laptops or anything else other than photo paper and film. Getting them to do this with photo paper and film is a lot more difficult than it used to be. I don't know if that's a policy or just unpleasantness cooked up at my local airport.

3) If you own a computer that has sensitive information on it, especially if you travel with it, I highly recommend that you use whole disk encryption. There are a number of players out there; the best one in my opinion is PGP. The best free one in my opinion is Truecrypt. I've used both extensively. The company I work for sells PGP software and I provide professional services associated with it.

4) If you travel internationally, US Customs and Border Protection has arrogated to itself the right to make you decrypt your laptop. They examine and sometimes take images of laptops once they are decrypted. Non-US border authorities also do this. They don't do this all the time, but frequently enough to be a concern.

PGP and Truecrypt both permit you to decrypt the hard drive but keep more sensitive files encrypted separately. With Truecrypt you can even have a completely hidden encrypted partition and operating system, while decrypting an innocuous and unused partition and OS for CBP to scrutinize.

While I haven't heard of CBP doing this, there are alleged cases of border authorities in other countries installing software on travelers' laptops for the purposes of industrial espionage. Whole disk encryption makes harder but not impossible; if you suspect your computer has been tampered with, reimage or reinstall it.