Hi Rich,
Welcome to community and thanks for using Fusion.
For resolve the issue, let's clarify some point.
The Shrink (Clean up the virtual machine) in General setting , it support following condition
1. MBR partition with NTFS formatted disk
2. The setting of disk should not check "Pre-alloctate disk space"
So if your disk are formatted as FAT32, or you check "Pre-alloctate disk space", the Shrink (Clean up) will not work. So you can check the setting of your disk first, see whether it supports shrink.
BTW, you check the "Pre-alloctate disk space" , it means that no matter you use the disk or not, it will occupy the space of you allocate to the disk. To make shrink work, after you delete some file, remember to clear the "Recycle bin", please let me know if you have any issue