Let me phrase better, Why was it working and showing new games i added, but reporting back to vita no free space? was the me messing up cl uster size?
Cluster affect how much space each files take up, NTFS use 4kb cluster and exFAT use 32kb cluster by default, but if you copy the same files to a NTFS drive and an exFAT drive, the 4kb NTFS would consume less space compare to exFAT, as for the vita, it would show you taken up more space if you use the smaler cluster, using 64kb cluster fixes the problem, where you see the correct size in windows, and molecular shell/ vitashell.