As you can see from the following snapshot the font (size) of the second (comparison) windows is different from the first:
How can I tell NP++ (compare plugin or general) to ALWAYS automatically use the font settings for first window for the second as well?
If this is not possible: How can I manually set the font (size) of the second window?
What version are you using? I remember a typo about the zoom factor being fixed in config.xml recently. I'd try again on a fresh N++ install.
Did you ever get this answered? I'm using the latest NPP, and have set every file type to use consolas, but it still makes the left side and right size of any view different font sizes, even if they are identical files and the specification file does not specify the font size.