My guess is that you have confused basis with capital account.

If you entered amounts under Partner Information > Partner Basis Worksheet for Adjusted basis at beginning of year (-1=none) (MANDATORY), these will flow through correctly to the Basis Worksheets of the respective partners but those entries have nothing to do with the capital account.

The amount for Beginning capital should be entered under Balance Sheet, M-1, M-2 > Sch M-2 (Capital Account).  This number will flow through to Cap Acct Recon.  On the third tab of the input screen, you will see the input screen for Special Allocations on which you can enter special allocations by either percentage or dollar amounts for capital account and other items.