Setting the property 'AllowMultipleValues' resets the control's type to "Lookup" when it is inherited from SPFieldLookup class.

When you develop a custom field type that inherits from SPFieldLookUp/SPFieldUser(not sure about any other controls) .
The derived field type has its own rendering controls. The issue arises when multiple values are to be stored in a field of the custom fieldtype.
In order to save multiple values to an SPFieldLookUp the property "AllowMultipleValues" should be set to true . When "AllowMultipleValues" property is
set to true, the field rendering control is overridden by MultipleLookupField. So the custom field rendering control is never instantiated/render if the field is
set to store multiple values(AllowMultipleValues=true). As a workaround what I did is overridden the ‘OnAdded’ function and edit the schema to append the ‘Mult’ attribute.

    1: using System;
    2: using System.Collections.Generic;
    3: using System.Text;
    4: using Microsoft.SharePoint;
    5: using Microsoft.SharePoint.WebControls;
    6: using System.Web.UI;
    7: using System.Xml;
    8:  
    9: namespace CustLookuColumn
   10: { 
   11:     public class MultiLookUp : SPFieldLookup  
   12:     {        
   13:        
   14:        public MultiLookUp(SPFieldCollection fields, string fieldName)
   15:             : base(fields, fieldName)
   16:         {          
   17:                    
   18:         }
   19:  
   20:        public override void OnAdded(SPAddFieldOptions op)
   21:        {
   22:            base.OnAdded(op);        
   23:            XmlDocument doc = new XmlDocument();
   24:            doc.LoadXml(this.SchemaXml);
   25:            XmlNode element = doc.FirstChild;
   26:            XmlAttribute attr = doc.CreateAttribute("Mult");
   27:            attr.Value = "TRUE";
   28:            element.Attributes.Append(attr);
   29:            this.SchemaXml = doc.OuterXml;
   30:            base.Update();
   31:  
   32:        }
   33:        public MultiLookUp(SPFieldCollection fields, string typeName, string displayName)
   34:             : base(fields, typeName, displayName)
   35:         {
   36:            
   37:         }        
   38:        
   39:         public override BaseFieldControl FieldRenderingControl
   40:         {
   41:             get
   42:             {
   43:                 BaseFieldControl fieldControl = null;
   44:                 fieldControl = new RenderFieldControl(); //See the below code snippet                               
   45:                 fieldControl.FieldName = InternalName;
   46:                 return fieldControl;
   47:             }
   48:         }
   49:     }   
   50: }

    1: using System;
    2: using System.Runtime.InteropServices;
    3: using Microsoft.SharePoint;
    4: using Microsoft.SharePoint.WebControls;
    5: using System.Web.UI;
    6: using System.Web.UI.WebControls;
    7: using System.Web.UI.HtmlControls;
    8:  
    9: //This is just a skeleton, I haven't included the entire functionality. 
   10:  
   11: namespace CustLookuColumn
   12: {
   13: public class RenderFieldControl : BaseFieldControl
   14:    {      
   15:        protected override void CreateChildControls()
   16:        {
   17:            base.CreateChildControls();
   18:         }
   19:  
   20:     }
   21:  
   22: }

    1: <?xml version="1.0" encoding="utf-8"?>
    2: <FieldTypes>
    3:   <FieldType>
    4:     <Field Name="TypeName">MultiLookUp</Field>
    5:     <Field Name="TypeDisplayName">MultiLookUpField</Field>
    6:     <Field Name="TypeShortDescription">Custom Multi LookUp Field</Field>
    7:     <Field Name="ParentType">LookupMulti</Field>
    8:     <Field Name="UserCreatable">TRUE</Field>
    9:     <Field Name="FieldTypeClass">CustLookuColumn.MultiLookUp,CustLookuColumn , Version=1.1.1.1, Culture=neutral, PublicKeyToken=6332f1922196b6de</Field>
   10:     <Field Name="FieldEditorUserControl">/_controltemplates/YOUR_LookupFieldEditor.ascx</Field>
   11:     <!-- 
   12:         YOUR_LookupFieldEditor.ascx is not included it would be identical to the ascx control under ..\12\TEMPLATE\CONTROLTEMPLATES\LookupFieldEditor.ascx
   13:     -->
   14:   </FieldType>
   15: </FieldTypes>

Note: The samples provided within this blog may not work, my intention was to provide you a workaround when you hit with this issue.

Happy customization!!!