So more testing and I was able to replicate it without Karbonite or K+ installed. If you have a ship in orbit around Kerbin and a ship around Mun, and you take a warp ship and warp to the Mun's SOI, your velocity goes down to zero. And then it keeps going down to zero every time you throttle up the warp drive. Nothing happens if you just jump around SOI's in a system with no other ships.