The true space something is using on your HD depends on the cluster size and therefor it can happen that you have a file that has a certain size and when looking at the space it takes on the drive it can give you a larger size.

I am not saying that this is causing what you are experiencing, but it may have to do with it.

Example:
Cluster size is set to 4096Kb
True file size is 5000Kb
Since the file won’t fit in 1 cluster it needs a second cluster.
So total disk space occupied is 2 x 4096 = 8192 Kb
And yes, this means that 3192Kb of the second cluster is not used and not available to other files.

Also keep in mind that 1Mb = 1024 Kb (and not 1000Kb as disk manufacturers wants to make you believe)

Can you tell us how you checked the space that is used?

Are you sure this is just the chest and not also the “infected files”, “user files” and “system files” section also?