Thank you very much for your message. Indeed, I have to confirm that the IV is the same for all files (or folders) created during a session in the current Boxcryptor for Windows version 2.0.405.295. If Boxcryptor is restarted, the IV changes. This is actually a bug and we will fix it asap in the next version which will be available soon.
Although this is not ideal, it is not a security risk because every file has its own random key. So no two files are encrypted with the same key. IVs are required if the same key is used for multiple files but if a key is used only for a single file, different random IVs are not required for security. For AES-CBC it is important that a combination of IV and key may only be used once - in our case this is the case even if the IV is reused over different files because each of the files has its own and different key.
I highly doubt that creating two different files with the same plain text results in encrypted .bc files which have the same cipher text (without copying the encrypted .bc files). It would be interesting if you could send the encrypted .bc files to email@example.com so that I can have a look at them.