Let me know if this gets you exactly what you need or not -- Table Calculations happen very late in Tableau's order of operations/pipeline, so the Filter you had created impacted the Table Calc since the Table Calc happened after the filter.
By using a FIXED LOD expression to create your filter, I believe we can resolve your issue -- take a look at the new formula for the "1% filter" and let me know if this gives you the result you wanted.
More info on why this works here, from Tableau's own Bora Beran: What’s new in Tableau 9.0? Part 2 – Level of Detail Expressions « Bora Beran
There were a few other measures and filters in place, so I just want to be sure the above is your expected output. Let me know if you have any questions. The FIXED LOD expression allows us to create the filter without impacting the Table Calc results (FIXED essentially means that your former WINDOW_SUM measure can now be FIXED to the total across the entire data set, and this FIXED expression happens before Dimension and Measure filters in Tableau Desktop, so the filter doesn't impact the percentage column you were concerned with) -- Study Bora's blog post on LOD for further understanding -- its a great resource!
The filter diagram on his blog is especially helpful:
Samplebook 2 ML LOD Example.twbx 18.2 KB