WB3.1 does not handle >4G partitions properly. They can work, but remaining space will always show as <4GB (it wraps around). If you keep filling it up, it will eventually wrap around when it reaches 0 and then show ~4GB free again. WB3.9 shows the correct free space (maybe also 3.5?).
It can be an issue if it shows very little space free and you are trying to install some software, as it will think it cannot fit. Then you can copy some files to it to make it wrap around, and then the installation will run.