Can you please attach the source code for your custom master page and for the page on which you want to change the master page.

Thanks.
Here they are:
1) ClipflairSmallHeader.master:
----------------------------------------
<%@ Master
Language="C#"
AutoEventWireup="true"
EnableTheming="true"
Inherits="MonoSoftware.MonoX.MasterPages.DefaultSmallHeader"
MasterPageFile="/MonoX/MasterPages/MonoX.master"
Codebehind="ClipflairSmallHeader.master.cs" %>
<%@ MasterType VirtualPath="/MonoX/MasterPages/MonoX.master" %>
<%@ Import Namespace="MonoSoftware.MonoX.Resources" %>
<%@ Register TagPrefix="MonoX" TagName="Menu" Src="/MonoX/ModuleGallery/MonoXMenuSimple.ascx" %>
<%@ Register TagPrefix="MonoX" TagName="Search" Src="/MonoX/ModuleGallery/MonoXSearchBox.ascx" %>
<%@ Register TagPrefix="MonoX" TagName="MembershipNavigation" Src="/MonoX/MasterPages/MembershipNavigation.ascx" %>
<%@ Register TagPrefix="MonoX" TagName="ClipflairPageFooter" Src="/MonoX/MasterPages/ClipflairPageFooter.ascx" %>
<%@ Register Assembly="MonoX" Namespace="MonoSoftware.MonoX" TagPrefix="portal" %>

<asp:Content ContentPlaceHolderID="cp" runat="server">
<asp:ScriptManagerProxy ID="scriptManagerProxy" runat="server"></asp:ScriptManagerProxy>
<link href='http://fonts.googleapis.com/css?family=Open+Sans:300italic,400italic,600italic,700italic,400,300,600,700&subset=latin,greek-ext,greek,latin-ext' rel='stylesheet' type='text/css'>
<div class="wrapper">
<div class="header-wrapper">
<div class="header">
<a href='<%= MonoSoftware.Web.UrlFormatter.ResolveServerUrl(MonoSoftware.MonoX.Utilities.LocalizationUtility.RewriteLink("/Default.aspx")) %>' class="logo"><img runat="server" src="<%$ Code: MonoSoftware.MonoX.Paths.App_Themes.img.logo_png %>" alt="MonoX" /></a>
<div class="membership-holder">
<MonoX:MembershipNavigation runat="server" ID="ctlMemership" />
</div>
</div>
<div class="navigation-wrapper">
<MonoX:Menu runat="server" ID="ctlMenu" UseSpanElementsInMenuItems="true" SelectedItemCssClass="selected" CacheDuration="600" />

</div>
</div>
<div id="main-wrapper">
<div class="main">
<asp:ContentPlaceHolder ID="cp" runat="server">
</asp:ContentPlaceHolder>
</div>
</div>
<MonoX:ClipflairPageFooter runat="server" ID="ctlFooter"></MonoX:ClipflairPageFooter>
</div>
</asp:Content>

------------------------

2) contact.aspx:

<%@ Page
Language="C#"
AutoEventWireup="True"
CodeBehind="Contact.aspx.cs"
Inherits="MonoSoftware.MonoX.Pages.Contact"
Theme="Default"
MasterPageFile="/MonoX/MasterPages/DefaultSmallHeader.master"
%>

<%@ MasterType TypeName="MonoSoftware.MonoX.BaseMasterPage" %>

<%@ Import Namespace="MonoSoftware.MonoX.Resources" %>
<%@ Register TagPrefix="MonoX" TagName="Editor" Src="/MonoX/ModuleGallery/MonoXHtmlEditor.ascx" %>
<%@ Register TagPrefix="MonoX" TagName="ContactForm" Src="/MonoX/ModuleGallery/ContactFormModule.ascx" %>
<%@ Register Assembly="MonoX" Namespace="MonoSoftware.MonoX" TagPrefix="portal" %>

<asp:Content ID="Content1" ContentPlaceHolderID="cp" runat="server">
<portal:PortalWebPartZoneTableless HeaderText='<%$ Code: PageResources.Zone_ContentZone %>' ID="contentPartZone" runat="server" Width="100%" ChromeTemplateFile="Standard.htm">
<ZoneTemplate>
<MonoX:ContactForm ID="ctlContact" runat="server"
A_WebSiteName="MonoX Demo" A_Address="Bihacka 1d" A_City="Osijek"
A_ZipCode="31000" A_Country="Croatia" A_Phone="+385 31 213 966" A_Fax="+385 31 213 967" EnableSSL="false" A_EMail="info@domain.com"
></MonoX:ContactForm>
</ZoneTemplate>
</portal:PortalWebPartZoneTableless>
</asp:Content>

---------------
NOTE: in contact.aspx I end up changing manually these two lines:
Theme="Default" --> Theme="Clipflair"
MasterPageFile="/MonoX/MasterPages/DefaultSmallHeader.master" --> MasterPageFile="/MonoX/MasterPages/ClipflairSmallHeader.master"

-------------------

I added your code to my project and everything works fine, but I don't have your custom control "ClipflairPageFooter.ascx" and your custom theme.

Is this page works ok, when you manually set the theme and master page on the contact.aspx page?

Hello again!
Yes, It works perfectly. The problem is that I end-up "hardcoding" my theme info for each existing page (like discussion.aspx, blog.aspx etc.

Shouldn't it be more automated? I must be missing something...

Now it works properly. :)
Thanks a lot for your time and advice :)

I'm glad that we solved the issue. :-)
Could you, please set my previous post as "answer", to can close the topic.