Hey! Sorry for the trouble.
Just making sure, what version of Sai2 are some of these files made on? It looks like there were some recent updates to Sai2 that might have changed how the file format works a bit, which I am still looking into at the moment and wanna be precise about what version you might be on. Do you see thumbnails for an Sai1 files you happen to have? Otherwise, are you installing the correct 64-bit version of SaiThumbs Particularly the one from the SaiThumbs-x64.zip file? Be sure to uninstall the previous version if you end up switching to the correct version to make sure there is no additional complexity. Generally the location of your Sai installation should not matter much, I personally have Sai2 installed on a separate drive as well, so that shouldn't impact the thumbnail generation. Though, it might matter what drive the SaiThumbs installation is on, and it will likely need to be located on a stable system-folder of some kind and not on an external drive.