I haven't seen the config not sticking, though I have seen a cached version of the config screen come up some times. Next time you think it's happened, can you check album.cfg directly? See if the changes were actually made, and just not displayed back to you...
The upload link is a known issue. I updated the code to try to be smart, and broke the link on the upload template in the process. Until I get it fixed, you can manually edit album_upload.tml and replace ####ALBUMPROG#### with a link to your album.pl. I'll fix that up soon...
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