The accessibility to the internal IP cores of Systems on Chip (SoC) provided by the testing infrastructures is a serious security threat. It has been known for many years that the scan chains can be exploited to retrieve secret keys of crypto-processors. Encryption of the scan chain content is one of the proposed techniques to overtake this threat. Many proposals are based on stream ciphers, due to their moderate area cost compared to that of block ciphers. Stream ciphers encrypt data serially with a keystream generated from an Initialization Vector (IV) and a secret key. Stream ciphers have a crucial limitation concerning the encryption of different data with the same keystream, called two times pad. Not enough caution in the IV and secret key management has been exercised in previous proposed works. In this paper, we show how the existing implementations can be exploited to perform a scan attack bypassing the encryption of the scan data. We also present a new implementation of scan chain encryption with a stream cipher, based on the IV generation by a True Random Number Generator (TRNG). Finally, we show that this new implementation is robust against the aforementioned attack.