Two Column Forms with Conditional Logic

This isn't a bug, but more of a limitation of what you can do with the Ready Styles. The styles are simply that, just helper CSS rules and there's no special logic applied based on whether the preceding or following fields are visible or not. When you're using conditional logic to show/hide fields, you may run into spacing or alignment issues depending on what's being shown or hidden at the moment.

Stepping back for a second, your first problem is the left padding on the list items in the form structure. That's coming from your theme. You should be able to add this to your theme stylesheet to override it.

[css]
#intro .gform_wrapper ul li,
#content .gform_wrapper ul li,
#footer .gform_wrapper ul li,
#features .gform_wrapper ul li,
#homerightcolumn .gform_wrapper ul li,
.sidebarwidget .gform_wrapper ul li {
    background: none!important;
    padding-left: 0!important;
}

As far as the 2 column structure with the conditional logic, I would suggest using some strategically placed HTML blocks to introduce some new markup/divs into the form as column container elements and then floating the new "columns" into place. With these as containers, you can drop the ready classes on those fields and they'll align normally within the new column.

You can find out more about what I'm talking about along with some examples on this previous thread. The member was trying to create a 5 column form, but the concept would still be the same for your application.

http://www.gravityhelp.com/forums/topic/how-can-i-get-the-form-fieldsboxes-side-by-side#post-29423

Wonderful. That's what I like to hear. Thanks for the update.