Unless you provide any further details like your page layout code or CSS you are using in page or are you using any custom page layout, people can't help you in an exact manner you have expected.
However, see my page layout code chunk as below. I have added 3 web part zones: header with 100% width, Left zone with 66% and Right zone with 33% width, and its working as expected:
<asp:Content ContentPlaceHolderId="PlaceHolderMain" runat="server">
<div class="welcome blank-wp">
<div class="ms-table ms-fullWidth">
<div class="">
<div class="cell-margin" style="width:100%;">
<WebPartPages:WebPartZone runat="server" Title="<%$Resources:cms,WebPartZoneTitle_Header%>" ID="Header"/>
</div>
<div class="ms-table ms-fullWidth">
<div class="cell-margin" style="width:66%;">
<WebPartPages:WebPartZone runat="server" Title="<%$Resources:cms,WebPartZoneTitle_TopLeft%>" ID="TopLeftRow" />
</div>
<div class="cell-margin" style="width:33%;">
<WebPartPages:WebPartZone runat="server" Title="<%$Resources:cms,WebPartZoneTitle_TopRight%>" ID="TopRightRow" />
</div>
</div>
</div>
</div>
</div>
</asp:Content>
You can also check if there is any CSS or other design components added in top zone web part affects your page layout structure.