In order to save the changes, you will need to update the xml file for that menu. In order to do that, open the menuStyle.xml file which is located in this folder:
CSSMenuWriter/cssmw1/menuStyle.xml
In the top of that file you should see an entry that look something like this:
<list-style-type>none</list-style-type>
<margin-top>0</margin-top>
<margin-right>0</margin-right>
<margin-bottom>0</margin-bottom>
<margin-left>0</margin-left>
<padding-top>0</padding-top>
<padding-right>0</padding-right>
<padding-bottom>0</padding-bottom>
<padding-left>0</padding-left>
<cursor>default</cursor>
<font-size>0</font-size>
and you should add the two changes, so it should look like this:
<list-style-type>none</list-style-type>
<margin-top>0</margin-top>
<margin-right>0</margin-right>
<margin-bottom>0</margin-bottom>
<margin-left>0</margin-left>
<padding-top>0</padding-top>
<padding-right>0</padding-right>
<padding-bottom>0</padding-bottom>
<padding-left>0</padding-left>
<cursor>default</cursor>
<font-size>0</font-size>
<position>absolute</position>
<z-index>1000</z-index>
This will ensure that changes stays after you reenter Menu Writer.