I’ve used beyond compare to synchronise two folders.
When I select the folders in Finder and look at the info the folders are different sizes. One folder displays around 8GB and the other 70GB. The folder of 8GB contains at least a folder of 8GB and 6GB.
How do I solve this conundrum? I’ve run disk utility and verified the disk is error free.
In reading this thread from the Apple discussion forum it hinted at hidden files being the problem and copying the data to another folder solves the issue.
I’m currently moving the folder and in so doing it is displaying the correct size.
edit: aded link to the thread I was talking about.
I’d jump into the command line and do things like:
du -hs ls -A
in the directory where you’re having issues. This is, after all, MPU and MPU can mean Mac Provides Unix 
(Edit: I didn’t see the last sentence of your response to yourself and I’m glad that fixed the issue!)