It looks like you are outputting the variable "Surface Window Total Glazing Layers Absorbed Solar Radiation" for each window. The two windows you mention have VERY similar names, but are different:
- ZN001WALL001WIN001SurfaceWindowTotalGlazingLayersAbsorbedSolarRadiation
- ZN001WALL001WIN0012SurfaceWindowTotalGlazingLayersAbsorbedSolarRadiation
The windows are both within the same wall of the same zone, which is why the initial "ZN001WALL001" for both output is the same. The easiest way to double-check this is to open the IDF in the Legacy OpenStudio plug-in for SketchUp and look at the geometry of the model.
To make post-processing easier, you can manually alter the names of the window surfaces to be shorter either in the SketchUp plug-in, IDF Editor, or a text editor with the IDF file directly. The SketchUp plug-in is the best method to apply a new naming convention to windows, in my opinion, because you can see window placement and orientation if you include that info in window names.