What Erik said.
This is in fact the source of the much-maligned 5-second increments - the game is taking smaller time steps in order to do what you suggest. The situation you describe means that the mechanism didn't work and the game took to big a jump in time. The intent is that the game should behave as you described - it pauses at the moment something (bad) comes into detection range so you can go to battle stations.
The way I work around this is to save the game often whenever I'm in a situation where I suspect combat might occur (e.g. probing a new system, or heading into a missile engagement). If the auto-sizing mechanism for time steps fail, then I restore the last save point and do exactly the same thing I did the first time, except I take smaller time steps (i.e. push the 1 hr button instead of 5 days). This is another example of the Space Master (you) helping the computer to get things right - the computer wasn't smart enough to advance the clock slowly, but you are.
One other thing: 5 days is probably too long a jump to use if you're in a situation where combat is likely. You're making it harder for the game to get things right.
John