How to track investments in Mint that aren’t on an online account

I've noticed what you're describing as well. At least with some sites, if they provide two-factor authentication, they ask you to verify factors beyond username/password from time-to-time. Generally, I've been able to resolve this by going to the site manually to verify my additional factors. Then when I refresh, the information updates again.

Two-factor security seems to be more and more prevalent with banking sites. I know Citibank does it for their student loan website. Vanguard does it for their site as well. Chevy Chase Bank (now owned by Capital One) does it on their website too, but I haven't had any update problems on that account with mint.com.

Mint Budgets uses averaging based on past spending initially. You are able to control the value of the budget for each category though. If you are on the Budgets page, hover over the specific budget you want to adjust and click Edit Details. A dialog will come up that allows you to set the frequency, amount, and whether or not the value rolls over to the next period. You can also delete an existing budget from this dialog.

On the Budgets page, there is a Create Budget button you can use to add a new category budget.