I enter a handful of securities that are in several different accounts hoping to get the net worth of those assets alone, and it gives me a number inclusive to other securities not selected.
Works for me. What version are you using? You need to of course choose the specific accounts and specific securities on their respective tabs of the customize dialog. Please double check those settings.
BTW, The account balances report may be better since I anssume you really only want asset values. Check the show details option on the Display tab to help see what is going on.
How about REPORTS, Investing, Portfolio Value and Cost Basis and then customizing the report to select only those securities?