It all comes down to accuracy
When a discrepancy is found, the one central question is: is it within, or outside, the uncertainty allowed by the inaccuracy of the calculation? Should we build a better computer model? Or do we need a better theory of physics? And the cycle repeats: improved models again need to be tested, constrained, vetted by the fires of empirical testing, and eventually broken and discarded to give way to even more detailed descriptions of Nature.
The achievable accuracy depends both on the sophistication of the simulation itself, driven by the development and implementation of new theoretical ideas, but it also depends crucially on the available constraints on the free parameters of the model. Using existing data to constrain the latter is referred to as 'tuning'. This is where the BOINC-based Test4Theory@Home project comes in.
