It looks like you set the FAF altitude for your departure and destination airports to 18000. I don't know if this is causing the problem but these should be left at their default setting of 0. The FAF altitude is not the transition altitude; it is the altitude to which you are cleared to intercept the ILS, and at the default setting of 0, PF3 uses 3000 ft AGL which works well in almost all cases. I would return the FAF values to 0 for KMDW and KCAK and retry the flight and see if that makes a difference.
Also, in the current version, the "Resume own navigation" call no longer occurs at the end of a SID. This was done on the recommendation of a RW air traffic controller on the team. You will get climb instructions but are under your own navigation to proceed to your first active waypoint.