Ok, that's really strange (but not unlike Presenter) that nothing normal works. In lieu of that, what you could do is publish the file to whatever crazy template Presenter seems to want to use and then go into the published folder and find the data/vconfig.xml file. Open this file in a text editor (such as notepad on a PC, or Text Edit on a MAC) and edit things here.
The lines that have to do with the colors of the template are at the top. I'm not sure how familiar you are with hex color codes but that's what you'll need to change. For instance on the first line for the primary color the hex number is 808080, which is a grey color. Make sure to leave the rest of the string alone and just change the last six numbers.
<colors>
<uicolor name="primary" value="0x808080"/>
<uicolor name="glow" value="0x0000D2"/>
<uicolor name="text" value="0xFFFFFF"/>
<uicolor name="light" value="0x4E5D60"/>
<uicolor name="shadow" value="0x000000"/>
<uicolor name="background" value="0xFFFFFF"/>
</colors>
As for the attributes and parts of the interface/template that you wish to display/not display, they are found in the next series of lines ...
<layout>
<uishow name="presentationtitle" value="true"/><uishow name="presenterphoto" value="false"/><uishow name="presentername" value="true"/><uishow name="presentertitle" value="true"/><uishow name="presenteremail" value="false"/><uishow name="presenterbio" value="false"/><uishow name="companylogo" value="true"/><uishow name="sidebar" value="true"/><uishow name="outline" value="true"/><uishow name="thumbnail" value="true"/>
<uishow name="notes" value="true"/><uishow name="search" value="true"/><uishow name="quiz" value="false"/><uishow name="attachments" value="false"/><uishow name="utils" value="true"/><uishow name="volume" value="true"/><uishow name="playbar" value="true"/><uishow name="talkinghead" value="true"/><uishow name="sidebaronright" value="false"/><uishow name="viewchange" value="true"/><uishow name="alwaysScrunch" value="false"/><uishow name="initialdisplaymodeisnormal" value="true"/><uireplace name="logo" value=""/><uireplace name="bgimage" value=""/><uireplace name="initialtab" value="outline"/><uireplace name="logo" value="logo.swf"/>
</layout>
Here you can just change the values from "True" to "False" or otherwise as needed. I know this is a long way to do things, and Presenter should certainly be able to publish to whatever template you choose, but hopefully this will get your project moving along. I personally have found that this is the only way I can get a template to do certain things, despite having chosen particular settings in the template I use to publish. The paper clip for attachments for example, is impossible for me to hide unless I go here and edit it's parameter to "False".
I'm going to ask this, and I know it's a stupid question ... but have you tried reinstalling Presenter 7? Or how about uninstalling version 7 and going back to version 6?