I noticed my Rat Loader acting flakey too. It doesn't show up in my Social Club garage, and when I tried to get in it in my garage, the entire game locked up. I can however have my mechanic bring it to me.
GT: LoneReaper115 Official Chaos Composite Bow of the Dark Souls message board
Noooooo! Mine went missing too so I tracked a new one down and when I tried to store it in my garage I got a prompt which reads "This vehicle cannot be stored in your garage." It was my favorite too :(