I tried using this on katawa shoujo, unsure if those files are simply too old or not. However, the error I got was access denied to the file location, since you have to drag and drop the file, not sure how you can get around this.
Feel free to share where the rpaExtract.exe is and where the .rpa file is in detail. Without knowing that I would guess:
1. .rpa file and rpaExtract.exe are on different drives -> move the rpaExtract.exe to the same folder as the .rpa file
2. the .rpa file is inside a .zip or .exe file and was dragged onto the rpaExtract.exe file -> extract the game in full before dragging the .rpa file onto rpaExtract.exe
3. the path contains non-ASCII characters -> move .rpa file and rpaExtract.exe to something simple like D:\rpaex\ and try there.
If nothing helps, which version are you extracting? The latest from the website works.