(chuckle) It sounds like your Home Port location has changed, which does happen in SHIV. Look for the icon with the tilted anchor, that's your Home Port. And, pay attention to your radio messages. They will (usually) inform you of the change. The regular anchors are your refit ports, the tilted anchor is your Home Port.
As far as completing objectives, if your patrol zone includes an orange star w/a pair of binoculars, you must remain inside a 50nm (I think) range of that star for 48 hours. If you go outside the 50nm range, the clock resets and you must start over again. At least, that's what I recall in the Stock Version.
Welcome abroad.
