If you dig hole with dirt and then try to fill that hole with the same dirt, you will invariably have some dirt left over. The dirt - which was very tightly compressed before - is now mixed with air, and poorly packed.
I think heart of the issue us that whole flax seed is hard and smooth, and will very easily slip into an efficient packing arrangement. Ground seed is fibrous and spongy and will initially pack very loosely as the various fibrous bits grab each other - it will not easily settle to a more efficient packing arrangement.
Given time and a bit of encouragement though, it will likely settle into a more compact form than the whole seed.
This is my opinion.