With OS3.1 you can not use more than 4 GB unless you install a different filesystem like Professional Filesystem or Smart Filesystem.
What I have been told is, that if you install a drive larger than 4 GB and start to use the storage space above 4 GB, then when you access the space above the 4 GB area the starting 4 GB gets overwritten. For instance in you case, when you format the second 4 GB partition, you damage data on your first 4 GB partition.
My advice is to create a 150 MB partition for Workbench installation (Workbench 3.1 only requieres about 8 MB, and OS3.9 only requires about 25 MB so it should be more than enough), and use the rest up to the 4 GB for a partition for use with games and applications. A second solution would be to install SmartFileSystem.
