By default, the user's settings are now most likely to be kept in... C:\Documents and Settings\
My Name\Application Data\Marine Aquarium 3
That's where my AltLogo.png and MA3Playlist.lst are. - Note that only the Beta9a will currently show the different clocks and calendar.
Ahh. I see now. The issue, if there is one, may something to do with an Installer, which would mean that it has little to do with us here.
After uninstalling both 2.6 and the 3 Beta I had been running (even using sachsremove.reg) and then installing both the commercial version of 3 and the Beta, I found two "MarineAquarium3" entries in my list of screen savers and assumed one of them had to be the Beta.
I failed to notice "SereneScreenMarineAquarium 3 B" farther down in the list: loading that brings up the clock. And putting AltLogo.png into \Application Data\Marine Aquarium 3 makes the alternate logo available.
Why there should have been two instances of "MarineAquarium3" I do not know: obviously the names could not have been identical, and I'm afraid I deleted one before making a note of exactly what it was called.