I'm the systems administrator for a research lab using Modeller 9v3.
While not the cause of the behavior you're seeing, 9v3 is really old.
Several bugs which in some cases affect the quality of output models
have been fixed over the past 3 years, and the latest version, 9v8,
should be entirely compatible with scripts written for 9v3.
I've installed the x86_64 RPM file on a pair of Xeon X5355 based systems
and some Opteron 6136 based systems. The researchers are reporting
getting radically different results between these two systems.
This is completely normal and expected. Due to differences from machine
to machine, floating point results will differ. While these differences
are very very small (say 10^-8), during an optimization of a rugged
energy surface they can end up giving very different structures.
(Imagine the system is at a local maximum on the energy surface, like a
ball at the very top of a hill. The tiniest push will send it rolling
down the hill to a local minimum. The "push" might be +10^-8 on one
machine and -10^-8 on another, but the local minima could be angstroms
apart.) These differences could occur because different processors order
floating point instructions differently (e.g. a*b*c could be evaluated
as (a*b)*c or a*(b*c)) or move data from memory to processor registers
(which often have a different precision) at different times.
Generally speaking, many models should be built for any modeling
problem, and something like the average of the best-scoring cluster
returned. Optimizations with the sorts of rugged energy surfaces common
in molecular modeling are very unlikely to find the global minimum if
only a single model is built. (Multiple models will also negate the
effects of differences between processors.)