I just pulled the barlow lenses off our microscope. They screw up the field of view and make it much harder to get a good stereo image. I can live with the closer working distance since the view is so much better. They also mess up parfocalality (is that a word) on the stereo scopes unless the eyepiece holders can be adjusted.
Interesting you should mention that as at first I just couldn't adjust the eyepieces to get a good view - moving my head up, down, left, right was causing blackness to appear, or the image became a small spherical area, etc. I'm getting the hang of it now but I'm still not 100% happy with the image due to this, I guess I'll continue to get the hang of it. That's with the 0.5x Barlow on it - I may try taking it off to see what the difference is.
Incidentally, if you're not using a Barlow which lens do you have on it? Just a 1.0x to protect the stereo lenses inside the scope? I understand that they can become permanently cloudy with solder and flux fumes after a period of time if they're not protected.