VirtualBox Disk Image (VDI) is larger than content but --compact doesn't work

I have a dynamic VDI image with 12 GB of data:

Filesystem      Size  Used Avail Use% Mounted on
udev            2.0G  4.0K  2.0G   1% /dev
tmpfs           404M  1.1M  403M   1% /run
/dev/sda1        29G   12G   16G  42% /
none            4.0K     0  4.0K   0% /sys/fs/cgroup
none            5.0M     0  5.0M   0% /run/lock
none            2.0G  148K  2.0G   1% /run/shm
none            100M   24K  100M   1% /run/user

However, my VDI image size was 32G. So I used CloneVDI.exe the first choice tool for cloning it into a smaller image. However, the cloned image still has a size of 21G, almost twice of what it should have. I have also tried VBoxManage.exe modifyhd --compact my.vdi without success.

What is the reason for this discrepancy and how can it be resolved?