I'm sorry. I must not have explained my situation clearly. None of my albums are password protected. I do not want to set individual album or user rights, if I can help it. I would like to use one password that I can provide to any person so that they can see the entire gallery. People without this password should see only a login page.
In version 1.3.1.2 the "options"->"gallery"->"Gallery password" setting in the admin panel provided this functionality, so that when a user logged in with the "Gallery password" they saw the home page, with thumbnails of each album taken randomly from the albums. In version 1.4.1.3, this same password allows the user into the gallery, but the album thumbnails on the home page are substituted with the err-passwordprotected.gif image. This is true even if I log in with my admin username and password, which obviously has access to everything, so this must be a bug.
I discovered a temporary workaround for this problem. If I uncheck the "options"->"image"->"Use lock image" option, then I get the desired effect. However, with this option unchecked, an album with a password shows a thumbnail, which breaks the desired security on that album.
I looked at the code, and while I don't claim to understand everything that's going on, I think I found the key difference between the two versions of ZenPhoto. In zp-core/template-functions.php, in the function printAlbumThumbImage (line 1395), the checkAlbumPassword function is compared to the token 'zp_public_access' (line 1430). This is different from the way it was done in 1.3.1.2. The problem is that the checkAlbumPassword function returns token 'zp_gallery_auth' when the album has no password, but the gallery does. Since it doesn't compare equal, the thumbnail created is the getPasswordProtectImage version, even though the user can (and should be able to) view the album contents.
As for the problem of the upload limit, I read about the php.ini options, and found a few settings that seemed appropriate. I set the options upload_max_filesize, post_max_size, and memory_limit all to 96M, but the problem remains. Any other thoughts? Both the jquery and flash versions only upload a subset of the selected images.