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Matus-

I too have an A-12, and spent considerable time trying to quantify the index error.  My suggestion is to move the tripod outside and eliminate the error assocoiated with the window.  In an ideal world windows would be optically flat, but such is not the case - particularly as the window ages.  Also - what size bubble are you using? Using very small bubbles (1/16") makes it easy to center the sun/star, but they tend to be a bit sluggish when it comes to resting at the top of the chamber.  Larger bubbles arent as sensitive to imperfections in the curvature of the glass.  Try 1/8".

My 2 cents - Paul