At the moment, if you try to upload an image for the file thumbnail that is the same size as, or smaller than, the minimum image thumbnail size specified in settings, then the default thumbnail is used rather than the uploaded one.
So far as I can see, there is no error message that tells you this is what has happened, so you end up, as I did, flailing around for ages trying to work out why your thumbnails 'don't upload' (they do, they were just too small/exactly the right size so the script didn't resize/upload them - it can only handle too-big images).
It would be *really* handy if the script uploaded smaller images even if they were smaller than/same size as the default. Or at least if there was an error message that popped up to say why the too-small image was not added. Or both!
The other thing I discovered while doing this is that because the way the image is called in the control panel is in the format 'wp-content/plugins/wp-filebase/wp-filebase_thumb.php?fid=11' rather than by filename - the first thumbnail image you put in is liable to get cached.
So then you are back to wondering why your replacement thumbnails 'don't upload' (they do, it's just that because they are not called with a unique filename, once you've uploaded one, you are likely to see that first one until you shift-reload, even if your second uploaded thumbnail had a different filename so normally would not be cached.)
Perhaps the thumbnail could be automatically cleared from cache during the upload?
These are small things in an awesome plugin which is really useful- many thanks.
I honestly have spent hours and hours trying to debug a thumbnail problem that doesn't exist! Probably I'm really thick to have taken so long to work this out - but both of these seem like small easy things to change that might help other users avoid that, so I'm suggesting them here. Hope this helps.