Many times there is more than one system used to track the same metrics. Many companies use their legacy internal systems to track revenue, margin, visits to their site, which they do not want to give up and also use the new systems like DART, Atlas to track the same metrics.
There will never be two systems which will track exactly the same. There will always be a discrepancy among the two, but the two big things are to identify what the discrepancy is and why does it exist.
Once identified the systems should track in the same direction - i.e. if one shows 20% increase in revenue the other should indicate the same.
In my experience, I think the best way to identify these issues is to map the data flows for both the systems. Once the data flow is mapped, then identity how much difference exists at each step. Also, it is possible that one system must have a longer cookie window than the other - this is a very common issue I have seen in the Online Marketing arena. So, these things could impact a lot.
One more thing I have noticed is that - sometimes systems are set to track a different level. For example: System A could be tracking at creative level and System B could be tracking at placement level. System A could be capturing only certain transactions (example - only certain product categories) but System B could be tracking everything. System A could be tracking only post-click data but System B could be tracking both post-click and post-impression.
One of the common example is trying to match Google Analytics Site data to DART Spotlight tag data. Yes, both of them are same company now but they track differently and never track the same. Some of the variables could be: session time, tags not firing correctly, tags not firing every time etc etc.
It can be a tedious process to identify the differences but once identified the reporting/measurement process becomes so much easy....