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After couple more days of working with it finally found the issue. I am using E+9.1 and had to convert the DOE reference building to this version. Somehow at some point of my work the E+ "OutputControl:Table:Style" object was set to "HTML" only. Where jEPlus+EA relies on .CSV output tables to extract the information for the analysis (sensitivity, optimization, etc.). So after changing the E+ model object to "CommaAndHTML" the issue was resolved (since now I get both .html tables and .csv which both are the same info just different format).

Note: This change needs to be done in the .idf (or the note) file and then imported to jEPlus to work.