A USB flash drive can contain anything. More specific, I keep a flash drive here with DSL (A small Linux Distribution) That will boot inside an emulator window or it can be booted directly from the flash drive. I also have a pile of various CD's and DVD's with Linux Live distributions. Some of them can be used to crack passwords and most of them can change, add or remove programs and files. These all boot from the CD or DVD drive and bypass any operating system you may have installed. To fix this, you can try turning off boot from CD/DVD and boot from USB falsh drive options. You'd also need to set an administrative password on the BIOS. Then, depending on which BIOS you have, there may or may not be a simple backdoor password to by pass it. Try and hope for the best. If possible, turn off running of any external programs from the CD or DVD and USB flash drives. Put a lock on the case if there is a way to do it.
Make sure his account in not an administrator's account. Make sure the hidden administrator's account has a secure password. You probably already did this, but it doesn't hurt to check.
Give him an ultimatum. If he bypasses the security, no computer for a week. 2nd offense 2 weeks. 3rd offense 4 weeks. 4th offense 8 weeks. If he makes it to a 5th time, 4 months. Since the punishment doubles each time, he can buy his own computer when he turns 18 if he tries a 9th time at 64 months. Remove the power cord and hide it to enforce this. Make sure no other cords can be substituted. A locking cabinet would be handy to store important parts of the computer. There are no exceptions. Not even for homework. He can use school computers for homework. If there is a problem with teachers, talk to them, explain the problem and why he can't use a computer at home.
With physical access to a computer, it is extremely difficult to secure it unless you can control everything it does and all programs are also secure and free of security holes. What is worse, he probably has a number of "friends" that are more than happy to help him break the restrictions. He could also be doing internet searches with Google and other search engines.
Shadow Wolf