This bug deals with the alignAxisToVect(vect, axis, factor)'s third input. A simple blend is uploaded with an example. This is in 2.49a
I'm not exactly sure how to describe what happens, it would be better if you download the blend and see what happens.
When the angle between the specified axis of the object and the desired vector is greater than 90 degrees the factor's value seems to rotate the object inversely.
Basically, what should happen, is that the greater the angle, the greater the amount of rotation that should be represented for a given factor. Instead, the bug makes the amount of rotation decrease as the angle gets larger than 90 degrees.
Did that make sense? If not, the blend should make the problem clear.