I am missing something for sure but is not system-xfree86-42 a virtual package? Why does it try to install x11 since Apple X11 beta 3 is installed.
It doesn't. x11 is a virtual package, provided by several fink packages. With the previous system-xfree86 package (which you have installed), x11 was provided by the system-xfree86 package. With the new version, x11 is no longer provided by system-xfree86, but by either system-xfree86-42 or system-xfree86-43.
This passage of a virtual package from one package to another is too tricky for fink's automatic update procedure, you have to remove the old package by hand (dpkg -r --force-remove) first and then install its new version again.
-- Martin
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