Matthew,
I'll admit it. I never noticed that the colors were different. But I can explain why and also how you can change it.
In SAS Enterprise Guide, we use the color-coded enhanced editor to display SAS logs as well as SAS programs. It just so happens that, out of the box, this viewer uses a different set of default colors for some log elements. I'm pretty certain that this has always been the case within EG -- nearly 9 years now. While it hasn't changed recently within EG, it is different from SAS Display Manager. I attached some images to this post to show the difference.
How you can change it: Tools->Options->SAS Programs. Click the Editor Options button. In the Enhanced Editor Options window, select the Appearance Tab. In the File Type field, select SAS Log File. Now you'll see a listing of elements in the middle of the window. You can select each one (Error, Warning, etc) and adjust the colors to your liking. I attached a third picture file to show the results in EG after I changed the options to the "traditional" colors.
Chris