Longer shutter speeds have absolutely NO EFFECT on flash exposure.
Depending on the power output of the flash, and I have the same SB800, you have anything from 1/250th at full power to about 1/50,000th at 1/128th power. This is the exposure speed the FLASH gives you, it varies with the power it fires at.
So, if shutter speed has no bearing on the exposure (provided you are within the synch speed) what does alter the exposure of the illumination given by the flash then?
The answer is your aperature. If you set the aperture on the camera to the same as the flash, then WHERE THE FLASH HITS you get a "correct" exposure. It is as simple as that.
Your barn and not being lit by the flash power, regardless of iso setting is due probably to the angle of the flash. Without some idea of the area involved we are all only guessing according to what we picture your scene as.
The SB800 is actually a pretty powerful unit - more powerful than the SB900 as it happens! The guide number at iso 100 is 38m - that becomes 54 at 200 and gives you about 1.4x the power/range/aperture. I think that is with the head set to 35mm from memory.
My guess is that you had the zoom set to too wide a coverage and there simply wasn't the power at that head setting for the area you were trying to illuminate.
Ways round it:
set camera up on tripod, set aperture at your working aperture, set shutter speed - if pitch black then it doesn't really matter, provided it is long enough for you to get inside the barn with the flash. Forget the commander mose and all that guff. Simply set the flash to manual and fire it with the test button, pointing at the bits you want to illuminate.
In pitch black, your shutter speed doesn't do a great deal - so providing it is only going to record diddly squat, it isn't having any bearing on the final exposure, only the light from your flash gun will. You can leave the shutter open, fire the flash at one bit of wall. Wait fo rit to recharge, fire it again at a different bit of wall on the same setting....until you have covered your subject. You will then get a properly lit picture, lit where the flash has hit, and next to nothing anywhere else - depending on the amount of ambient that can creep in through your open shutter.
If you use the SB800 on A mode, then you can set the flash to the same aperture as the camera and it will adjust the power of the flash depending on your distance to the subject you are firing it at....on manual, you will over expose if you are too close and underexpose if you are too far away. There is a rough distance scale on the LCD to get you near enough the right distance.
Hope that helps. - oh, and set the flash head zoom to about 35 or 50 - it shortens the recycle time. If you ask it to illuminate a great wall of a building on 24mm, you are really making it squeak and it will probably not be able to put enough light in the entire coverage, so you will get fall off on the edges of the flash coverage. You can actually use this to give graduated results if you want to.
So for the kind of thing you were trying to do - old fashioned simplicity is best. Modern auto everything can't cope. And I am a bear with virtually no brain that can't work a mobile phone!