You have to set the CSS for your navigation in the main.css essentially the navigation is presented as an unordered list and the main part that gets rid of the bullets is:"list-style-type:none;"

Here's what I usually use:
[
#page #header #headerNav{
float:left;
width:100%;
overflow:visible;
list-style-type:none;
line-height:2em;
display:block;
}
#page #header ul.nav-header{
list-style-type:none; margin:0px; padding:0px; width:auto; overflow:visible; float: left;}
#page #header ul.nav-header li{float:left; padding:0px; margin-left:20px; margin-bottom: 0px; color:#42686b; font-size:14px; margin-top:0px }
#page #header ul.nav-header li a{ text-decoration:none; color:#669a99;}
#page #header ul.nav-header li a:hover{ text-decoration:none; color:#42686b;}
#page #header ul.nav-header li.nav-selected{ color:#42686b; font-weight:bold;}
]

But I've already done this and It's still got the bullets. The top navigation to the website works just fine and is styled from that code but if you "move" or add the navigation to the Main page of the website in the default theme the bullets show up again.

I wish I wasn't working locally so I could send u a link.
I hope that makes sense.

I'm in the same boat.

I'm trying to do a simple two column vertical list menu. I used the list-style-type:none; on my CSS but the bullets remain as does the indent though it is set to none.

Any suggestions?

http://www.gootlawd.com to view

as craftyCS said its the list-style-type

i believe it is set in the block's styles if you make a custom template you can point it to a different css file that excludes that line