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SWMM 5.1 Results differ from Sewergems SWMM Calculation Results

I am getting a -21.0% Flow Continuity Error in my Sewergems model so I exported it and ran it in the SWMM 5.1 software and got a -0.16% Flow Routing Continuity Error.

I'm wondering what could cause such a drastic change in results. 

A few notes. The model has two ponds modeled and one outfall. One inlet that is upstream of the pond has a -800.76% continuity error for it's surface node (in sag inlet - "Node 828f_Surface). Obviously this is causing the most problems but I'm not sure how to fix it since the inlet is not overflowing or surcharged. The rest of the nodes listed in the "Highest Continuity Errors" section within Sewergems are in the 9-36% range. 

I am using Sewergems CONNECT Edition Update 1 (10.01.01.04) within Microstation V8i SS4 and EPA SWMM 5.1.012. I will try to upload the "Outfall D6_NEW" file for reference. 

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