I'll have a look at this tomorrow, but for now it would be really helpful to know the steps to reproduce the issue in a project with just NGUI present rather than a whole project to look at.
I've zipped just a test project sources without any other extensions. Very clean and tidy. But i've excluded NGUI package of course as you've asked (we use licensed version)
Steps:
1) Create Bitmap Font 1 with NGUI FontMaker size 20
2) Create Bitmap Font 2 with NGUI FontMaker size 24
3) Create UILabel1
4) Create UILabel2
5) Set UILabel 2 font, font size - 20, effect outline with black and 175 alpha, align left, pivot center-center
6) Set UILabel 1 font, font size - 24, effect outline with black and 175 alpha, spacing x -1, align center, pivot center-center
7) Set UILabel 2 anchors to Advanced
8 ) Drop UILabel 1 to top and left anchor fields.
9) Move UILabel 2 a little bit with keyboard arrows and mouse. (strange anchors behaviour could be seen even here - numbers not always get updated)
10) Now just set random text to both text fields at runtime