Trying to help a client (home builder) figure this one out. 

In a home facing SouthWest, a room will often reach temperatures in excess of 30C. The home was new build in 2019, occupants moved in in 2020. Window measured 96"x68", two operable casement sections with a large picture window in the middle. Picture is rated with an SHGC of .57 and casements with .46. I've check using a EDTM solar transmission and power meter, the solar transmission was out 57-58 so right in line, but when I switched to BTU/Sq foot, it rose up to 132. The home had an HVAC design that used  a .45 SHGC window (builder didn't update designer in between). LowE is on surface 3. Even when calculating everything for this room, it shouldn't be reaching the temperatures it does. When looking at it through a thermal camera, the glass even with curtains open is 95F on the interior. Some of the surfaces the sun strikes are also being heated beyond into the 90's and in some cases over 100F. 

Looking for thoughts as to what might cause the excessive gain as even when using plain glass the room shouldn't be able to heat up as much as it does.

Is there a chance the window glazing's (Ie: LowE surface) got installed backwards? 

30-35C surface temperature for a window in direct sun doesn't surprise me.  Where's your math?  A SW-facing window can be expected to absorb 200W/m^2 in direct sun during the afternoon and evening.

As I wrote above, full sun on a clear day is about 1000W/m^2, or 317 BTU/hr/sf.  For glazing with a 50% SHGC, you should measure around 150BTU/hr/sf.  Given the readings you are reporting, is sounds like your EDTM meter is crap.

I live near 45 degrees N.  On this mostly sunny afternoon when the sun was around 215 degrees and shining into my SW-facing living room window, the glass temperature was 26C.  The outside air temperature was 2C, and the surface temperature of my living room coffee table was 50C.  The window is double-glazed clear 3mm glass.