i would suspect that a call is randomly placed onto a physical resource (between RNC and core network) which is not properly configured. The same as a one-way call.
Ciphering problem should not happen randomly, I think…
does it happen on all brands of MS ?
did you configure E1’s link somewhere ? perhaps one timeslot of those E1’s is configured to carry signalling, whereas it carries traffic in reality.
The “randomness” of the problem is a lead 🙂