Every time you tighten a string, it slightly de-tunes all the other strings.
This effect is more pronounced, depending on how large the adjustment.
By going through the strings 4 or 5 times, I am finally able to tune my guitar to my satisfaction.

Start by setting the Delay to 8.
Now click on auto-advance, or just hit the space bar.
Once you've gone through the strings twice, change the delay to 3.
Continue tuning until you no longer need to make any adjustments.
You are now tuned!

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Guitar Tuner courtesy of the folks at Wimpy Player