The fact that all partitions are visible is 100% intentional (censoring the partition table makes it even more confusing for users, and unnecessarily hard for VirtualBox itself). It doesn't mean that you can read from or write to them. Reading will produce zeroes, writing will be ignored.
Also, the only way to tell if there is really something wrong with raw disk handling is providing the .vmdk file in addition to the partitioning information.
