It looks like you ioncube library installed into /home/ioncube/ioncube_loader_lin_5.3.so.
What Flavor of Linux are you running?
on my centos (redhat variant) .so files are in the /usr/lib/php/modules directory.
It looks like your distro may normally put them in /usr/local/lib/php/extensions/no-debug-non-zts-20060613/
Is there a symbolic link to the file which resides in "/home/ioncube" placed in that directory? If so, just removing the link and putting a copy of the actual file there may solve the problem.
good luck.
fZ