Uh, strange. Maybe it's the file settings.json (that keeps the swatches) that's corrupted...
You can try to delete it (after send it to me (dunin(at)laposte.net) so I can debug the program). The location of the file depends on the OS and whether you use the itch application.
For example, on windows, it is C:\Users\yourUserName\AppData\Local\Paint Of Persia\User Data\Default\settings.json