I am having the exact same issue. When I put sepratrons on an S1 SRB attached by hydraulic manifold to an orange tank, the sepratrons fly off unexplainedly. Additional information: When I separate the SRBs shortly after launch (running or not), they separate just fine, and the Sepratrons don't fly off. However, when they're almost out or completely out of fuel, the Sepratrons fly off. Pre-firing them prior to decoupling doesn't help, since as soon as the hydraulic manifold decouples, the Sepratrons decouple. The problem DOES NOT occur if you use TT-38Ks or TT-70s, so I believe I've narrowed this down to an issue with the hydraulic manifold part itself. My advice would be to just not use that part until Squad fixes this little bug. I tested this with several rockets, but all used the orange tanks for attachment. Here's the one I did the most testing with: