PSTL Fiscal Year Modifier

I used the PSTL Tool to modify my fiscal periods. I reconciled the financial years before I ran the tool and again after I recreated my fiscal periods. The Income Statement is correct for each year, but the Balance Sheet is not. As I recreated my fiscal periods I calculated each year, marked all the periods/modules closed and checked the box for Historical year on each year that was historical and then created the next year. Both times I reconciled I started with the oldest year first and came forward to the Open years. Luckily I am working in a test company but I have to have this resolved before the end of the month. We went from having a fiscal year of 10/1 - 9/30 to 1/1 - 12/31. I am creating a short year for 10/1/2013 - 12/31/2013 and calling it 2013. Each prior year had to be renamed so that the year corresponded to the Beginning of that year instead of the end of that year. Example, 2013 before the PSTL Tool use was 10/1/2012 - 9/30/2013. Now 10/1/2012 - 9/30/2013 is year 2012. What could be wrong with my Balance Sheets not matching my Balance Sheets prior to the use of the tool? Should I have opened up all the closed years after recreating the fiscal periods and before running reconcile?

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