Gargan

I was having the same problem as OP where one of my outer stage's sepratrons were not firing during that stage's decoupling. I even replaced the sepratrons with Ullage motors from KWR thinking that might help, but no go. I was always under the assumption that the order within the stage had no effect and thus no reason for me to worry or bother. After verifying that they were correctly staged and a multitude of testing I started searching around for sepratrons not firing and found this post. And I can decidedly say that rearranging the order such that the sepratrons were above the decouplers is what fixed it. I never restarted KSP throughout this process and the only thing that worked was the rearrangement. This has to be some type of bug in how each part within a stage is set off. It also might have something to do with how many parts total are being simulated as my setup is rather large and starting to slow my simulation time down a bit. I wonder if that is why one of my inner stages with sepratrons has always worked as expected, irrespective of order within the stage. Maybe once the simulation starts to slow down with all the physics calcs some sort of timing issue pops up. I don't know, but I just want to say thanks for at least helping me out with this issue I was having.