What do I do if I have very carefully been saving, entering into the register. When I do a profit and loss report there are entries that are not appearing,

What register? What type of account is it?

Entries will usually appear if they use income/expense (P&L type) accounts. Those that use other balance sheet accounts won't appear. For example, a loan payment using a liability account (the loan) won't appear as it's not an expense.