I'm sorry that you're having problems using BoxCryptor. Can you please answer the following questions?
1) Where did you store the files and where do you try to open the files? In the BoxCryptor Folder (e.g. \Dropbox\BoxCryptor.bc) or in the BoxCryptor Drive (e.g. X:\)?
2) What software did you use to store and/or copy the files? Windows Explorer?
3) What type of files are you having problems with and what is the exact error message? (Maybe you can provide some screenshots)
If you uninstall BoxCryptor, the BoxCryptor Drive will not be available anymore. Files will stay encrypted in the BoxCryptor Folder and can be accessed in the BoxCryptor Drive at any time again if you re-install BoxCryptor, open the existing BoxCryptor Folder and enter the correct password.
PS: If you did not uncheck "Remember password" when creating the BoxCryptor Folder, you will not be asked for you password on this device. If "Remember password" is unchecked, you will be asked to enter the password every time the BoxCryptor Drive is created.