Skip C, I am currently using CCleaner Pro 1.15.507 on the latest Mojave beta 10.14.1 (build 18B45d) [note this beta was released after Mojave went public] and I cannot replicate the issue you're experiencing with resizing the application. Upon changing the window size and close CCleaner, the app retains my recent changes.
You may want to try booting in Safe mode to see if you can save the window changes then. If so, then another application is causing the issue.https://support.apple.com/en-us/HT201262