The quick and easy answer is to override the ending balance by making an entry in the ending column of the Balance Sheet input screen.

ProConnect automatically generates the ending balance by taking the beginning balance per balance sheet input screen, adding any current-year additions recorded in the depreciation input screen, and subtracting any current-year dispositions recorded in the depreciation input screen. There should be a worksheet showing what it thinks are current-year additions and dispositions. You should be able to identify the issue from that worksheet.