Well, I looked at the .xojo.xojo file and the key you mentioned was not in it. but even stranger, it was a truncated file, only 19 lines long and not a complete XML file.
I altered the file to the point Xojo wouldn't read it. It asked me to download my license key, which I did. I then opened a new project, saved it and the .xojo.xojo file was now complete ( about 122 lines ). It had the Window position key with the position: -7, -13, 1088, 611.
(Why negative numbers?)
As a test, I edited the numbers to -7, -13, 988, 411 and the saved empty project. It then opened with the new size. I opened and saved my actual project and the .xojo.xojo file is again truncated to 19 lines. Could there be something in a project file that couls do this?
For the moment, opening the project in an old version and resaving works, so it's not super critical, but maybe of interest to Xojo.
I'll paste in the truncated file at the end.
Thank you for your help,
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<string>Courier 10 Pitch</string>
<key>Control Font Size</key>
<key>License Agreed v2</key>
<key>Recent Items Dict</key>