@kseistrup: Permissions here are the expected 0755 and 0644, this is what I can currently see in my system with the latest versions of the packages installed:

% ls -l /usr/bin/lowdown{,-diff} /usr/lib/lib{diff,lowdown}.a 
-rwxr-xr-x 1 root root 112648 ago 24 14:59 /usr/bin/lowdown*
-rwxr-xr-x 1 root root 112648 ago 24 14:59 /usr/bin/lowdown-diff*
-r--r--r-- 1 root root  38120 ago 24 17:32 /usr/lib/libdiff.a
-rw-r--r-- 1 root root 191764 ago 24 14:59 /usr/lib/liblowdown.a
%

Could it be that you have your umask changed to some non-default value?

PS: I believe the guy behind lowdown/libdiff does something we don't do on Arch: He installs executable files as 0555 (we usually use 0755) and other files as 0444 (we usually use 0644).

I've pushed the update to version 0.4.0 a moment ago.

@kseistrup Thanks for the heads up about libdiff! I got a PKGBUILD for that done as well :-)