I have experienced a problem that others in this forum have also experienced: reconciling cash accounts when the same investment exists in two or more sub-portfolios. The problem is enhanced when you have more than one cash type investment assigned to the same sub-portfolio. You know you have the problem when you reduce or eliminate shares in one investment and the cash account doesn't change, or it changes in an unstable way.
To expose and diagnose these type problems, I and staff have begun a huge effort ( 5 portfolios, each containing about 30-40 investments, at least 2 years of many transactions) of reconciling each portfolio each month for the past 2 years.
A piece of advice to users: When setting up and entering any sub portfolio append an i.d. suffix to the investment. e.g. say IBM is in more than one sub-portfolio, enter IBMp1 into port no.1, IBMp2 into the 2nd, etc, do NOT use IBM without any suffix. Also stick to one unique cash-type account per sub-portfolio. ( and if you transfer the investment between portfolios, e.g to meet m.r.d. ira req's - sell the investment in the transferring acct, and buy it in the transferred to acct.)
A simple software addition could make this reconciliation effort much easier: enable the wizard to reconcile on a selected date, not simply on the current date, for a manual reconcile only.