Start by checking, if your save games are there at all.
Steam is using cload save game location, so you cannot deduce anything from steam games working.
Itch uses a dubious installation path for exe, and the games use whatever save game location they use. It is dubious, because it installs exe in appDATA .
But most games on itch are "portable". Meaning, that you unzip and run, and save game location is in relative system path, like those user directories. So they should work. But itch is basically using the same mechanism to find the games, as the games use to find their save games. And if itch can't find the games...