I'm not sure that the changes made in 3.0 could alter the css of your ul/li - in fact I highly doubt it. However, if it only just recently showed up ("out of the blue"), it seems suspect (3.0), doesn't it?
Unfortunately, if you aren't comfortable with the coding side, there is not much you can do...except go to the code and make the changes since I don't know what editor you use.
For your reference:
"style.css" - This is the file that, in your specific case, handles the majority of how things look on your website. It handles the grand majority of spacing, colouring, font, meta-data, and more.
My best guess would be that a change was made to an option in your visual editor that changed the ul/li code. Double check your settings. Also, if you have access to your website by FTP (you should), a very simple work around would be: delete the file named "ul-bullet.gif" from the "images" directory. This will force all browsers to default back to a regular bullet-point, but won't affect the spacing issue.
Hope this was helpful :)