1. First a digression
(ISO seems to be the confusion, so lets start with getting that out of the way)
The true and sober answer to your question is that: "IT DEPENDS".
Because the fact is that your camera actually has an advanced feature called ISO Sensitivity Auto Control which you can turn "ON", and which enables your camera to automatically vary the ISO factor.
Shooting in low light (e.g. an event) you can with this feature instruct your camera about:
- a selected maximum ISO value, and
- a selected minimum Shutter speed
So when you fire away at your chosen Aperture value (and preferred ISO value) you camera will first choose to adjust the Shutter speed.
But if it hits your selected minimum Shutter speed limit, then it starts increasing the ISO value right until it also hits your selected maximum ISO value limit.
At this point the camera has no other choice than crossing the line for your selected minimum Shutter speed and use a slower speed. And that's what it will do.
Some day you can read more about that at p. 166 in your D90 Manual.
It's a brilliant and intelligent feature for certain tasks. But the good thing is that right now you can just forget all about it. For your HDR purpose you don't need it (though you still can use it). Just turn the feature OFF.