I am very new to this, and I do not understand much about computers.

Ever since yesterday, some programs would not launch. I double-click it, but nothing pops up. Most programs work, but some wouldn't start. The best I could do was run a virus scan with BitDefender; I found two infected files found in C:/Windows/System32 that could not be disinfected or deleted (Sorry, I forgot to save the names of these files).
I have NO IDEA what is going on, so can you please tell me what I should do?

What you are doble-clicking is the shortcut to a program. If the program file is missing (uninstalled) that doesn't necessarily mean that the shortcut is removed too. Usualy the programs are installed in such manner that an "uninstall" icon is placed right under a progeam icon in a "programs" group and can be uninstalled by mistake. My suggestion is to try and uninstall the programs in question and install them again.
The 2 infected files should not worry you. It is probably a spywaer or an adware. To get rid of them disable the virus shield (right click on the BitDefender icon in a tray) and manulay delete the 2 files. If you can't delete them this way, that means that they are being used by the system. Ctrl-ald-del will open a task manager. Click on te "processes" tab, click on the "Image Name" column header to sort the processes by name and use the file names of tfose files to figure out which proccess is to be manualy ended (right click on that process and select "End process"). It could be 1 or 2 proccesses. Usualy, the file name is the Image name also. After processes have been ended, delete the files and reenable the virus shield.

One more thing about BitDefender. The newer updates are availabe on the hourly basis, so the manual update every now and then is adviced regardless of automatic update setting.

It seems to work if I reinstall them, but the same thing keeps happening. I tried reinstalling my windows, but the problem is still persisting. Sometimes, I can't even uninstall it, because the uninstall windows won't show up either.

If you can not uninstall the program thta doesn't mean that you can not install them again. They are, probbably, just uninstalled by accident. And I you reinstalled the windows, then you have to install ALL of them again. All the install/uninstall record is kept in windows registry, that was deleted by windows reinstallation.