Yep I've been getting the same exact issue. I noticed this bug initially in v0.23 I think.. or whichever was the first release that had career mode with contracts. Tried running both x86 and x64 for several different releases (in Win7) and it occurred just as MajorThomas has described above in pretty much all of them. Also had this bug come up in tandem with the docking port bug when docking ports refused to 'undock' and eventually after poking around long enough, the flight would disappear. Extremely disappointing because up until release 0.22 the game was bulletproof for me. I suppose it's the downside of adding layers of complexity as you go rather than planning all functionality before development. Especially painful to experience the bug in career mode as it can end up in bankruptcy Hope they manage to address the issue in later releases, it's a brilliant game.
