I am using Script Manager with Google Analytics and have continually found inconsistency with the tracking. Recently I was running some tests in Google Analytics Real-Time and I found that when I click on my Unbounced landing page GA is not tracking an Event and counted my session as a bounce. Thoughts? Fixes?
When it comes to tracking and analytics, no 2 tools are ever going to show the exact same numbers.
Now keeping the above in mind, you have to account for at least 4-5% discrepancies and sometimes up to 10% or more. Depending on the particular setup.
If you are seeing more than 10% difference, I would strongly urge you to do a full analytics audit.
There are simply too many possible explanations for a discrepancy to be able to point you in the right direction from a simple community post.
You need to start inspecting what is being fired when and what data is being pushed out to Google Analytics.