I have sucessfully landed the STS-26 mission with a Chandra satellite sticking 45 degrees up from the payload bay. Seems funny, but bug happened: computer gives me a command to rise the satellite for launch, I comply. Then I am given the comm to position a Shuttle at the angle for satellite launch. Here all difficulties start, I enter PYR values from the checklist, they don't work (perhaps were made for earlier versions of the game), I am trying to position a Shuttle with a joystick (I am flying with a flight stick) and each time the yellow horizontal bar passes the central ADI horizontal reticle nothing happens. Then I get a command that satellite already at Stage 1. Then a command to prepare for deorbit (while satellite is still sticking, I guess that rise button does not foresee the possibility to lower the payload bay cargo). Fine, I follow all the commands, stow the radiators, KU antenna, close the payload bay (with sticking satellite) and go for re-entry sequences. Landed successfully and satellite was still sticking up with Shuttle already standing on a runway with a mission complete status and badge in achievements. Though in reality such de-orbiting and re-entry would have been a disaster.
So, basically, if computer orders you further sequences follow them and go for de-orbit, re-entry and landing. If it shows "No-go" then you might wait until Shuttle completes a new orbit and COMM might change, but if that does not happen and you are already in deorbit procedures - then you should restart the mission, or load an earlier save where the problem could be still fixed.