It wasn't a 95%/99% of the satellite making it; those were the chances that there wouldn't be an incident with the ISS if the upper stage activated.
The Falcon 9 ended up in a slightly different position/velocity than was expected, and the primary mission (deliver to the ISS and don't dare run anything into it) took complete priority over the secondary mission of launching the other satellite into a high orbit.
That simply doesn't make sense. The OrbComm satellite was almost sure to burn up if they didn't launch it from a higher orbit. If the only risk was to the satellite, then go high or go home.
The problem was a (very small, almost surely overstated, but there nonetheless) risk to the ISS. From Orbcomm's press release: "the rocket did not comply with a preplanned International Space Station (ISS) safety gate to allow it to execute the second burn."
The Falcon 9 ended up in a slightly different position/velocity than was expected, and the primary mission (deliver to the ISS and don't dare run anything into it) took complete priority over the secondary mission of launching the other satellite into a high orbit.