Yup, sometime in the 2000's Strasburg started returning their locomotives to a "Heritage" look, making them look like they did when in operation on their original railroads. I believe they were paid to do that.
31 was changed back to 7312 and given a Canadian National (CN) logo on her tender.
89 had her "high" headlight removed and was given the CN Center Headlighthttp://www.auralorgasms.com/, lighted number-boards above the headlight and CN style number-plate below and the slanted CN logo on her tender.
90 was restored to close to her late 1930's appearance which included a Pennsy style headlight.
475 was returned to her Norfolk & Western appearance.
They stayed like that for a period of time until they decided to keep the "Heritage" look but to label them for Strasburg, using the predecessor road's scheme/font etc.
Since then, I believe only 90 has had any significant changes to her appearance, getting a repaint in early 2014.
-Mark