I am doing something wrong, it seems.
I am no great Photoshopper, but I did what you said to do using two methods;
1) Create a layer from the grey boxes and then change the opacity of that
2) Select the grey boxes and use the Fill function to change it that way.
On both occasions, when I replaced the file, zipped it, renamed it and put it into REAPER; REAPER just defaulted to its most basic theme. So I must be doing something wrong.
I have attached my file.
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