This is relevant to Quicken using one Quicken data file. I don't know some of the answers, specifically rental properties. We probably need more info of what/how you're doing it now to be helpful for you. What version do you have?

Your incomes should be setup as a "paychecks".

Your 2 homes should be set up as property accounts (maybe your rentals too).

Each taxable brokerage & IRA's should be set up as individual accounts in the one data file. I assume this is true for an SEP but have no practical knowledge SEP's.

So, are you using one data account?
Can you give us an example of one of your inputs to an account (fictious info is OK, it's more the method that's important).
Are D/L'ing data/statements from banks/brokerages and this is where your issues are? I've gotten away from doing that since I always had reconciling issues. I now input the data manually from statements. I think Kurtv favors this method too and he'll probably be along soon with input for you.

You should try searching the Quicken Help files and Quicken dot com for guidance. Sometimes they are very helpful, other times....

I don't find that many program updates from them so I don't understand why you think there are "so many" glitches from updates. You can do manual updates by D/L'ing the update files from their site and then installing them.

Sometimes it's the old GIGO (garbage in - garbage out) and maybe you're just recording your inputs incorrectly.