I've managed to narrow down the problem.  [TestFixtureSetUp], [SetUp]
and [AssemblyCleanup.Setup] do get run before the [CombinatorialTest],
the problem is the startup code for the [Factory] method  is run before
any setup methods.

Is there any way to fix this?

See demo:

using System;
using MbUnit.Framework;
[assembly: AssemblyCleanup(typeof(MBUnitDemo.AC))]
namespace MBUnitDemo
{
    class Program {
        static void Main(string[] args){
            using (MbUnit.Core.AutoRunner runner = new
MbUnit.Core.AutoRunner()) {
                runner.Load(); runner.Run();
                runner.ReportToXml();
            }}}

    public static class AC
    {
        [SetUp]
        public static void SetUp(){
            Console.WriteLine("AC Setup");
        }
    }

    [TestFixture]
    public class Tests
    {
        [Factory(typeof(string))]
        public System.Collections.IEnumerable GetSomeTestItems()
        {
            Console.WriteLine("In GetSomeStrings startup - this does
not show in report");

            yield return "s1";
            yield return "s2";
        }
        [TestFixtureSetUp]
        public void TFSetUp()
        {
            Console.WriteLine("TF Setup");
        }
        [SetUp]
        public void SetUp()
        {
            Console.WriteLine("Setup");
        }
        [CombinatorialTest]
        public void CTTest([UsingFactories("GetSomeTestItems")]string
ti)
        {
            Console.WriteLine("Test " + ti);
        }
    }
}

  <?xml version="1.0" encoding="utf-8" ?>
- <report-result xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:xsd="http://www.w3.org/2001/XMLSchema";
date="2006-11-29T18:15:50.8107502-05:00">
  <counter duration="0" run-count="2" success-count="2"
failure-count="0" ignore-count="0" skip-count="0" assert-count="0" />
- <assemblies>
- <assembly name="UnitTests.MBUnit"  full-name="UnitTests.MBUnit,
Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
- <set-up name="MBUnitDemo.AC.SetUp" result="success" duration="0"
memory="24576">
  <console-out>AC Setup</console-out>
  <console-error />
  </set-up>
  <counter duration="0" run-count="2" success-count="2"
failure-count="0" ignore-count="0" skip-count="0" assert-count="0" />
  <version major="1" minor="0" build="0" revision="0" />
- <namespaces>
- <namespace name="MBUnitDemo">
  <counter duration="0" run-count="2" success-count="2"
failure-count="0" ignore-count="0" skip-count="0" assert-count="0" />
  <namespaces />
- <fixtures>
- <fixture name="Tests" type="MBUnitDemo.Tests">
- <set-up name="TestFixtureSetUp" result="success" duration="0"
memory="0">
  <console-out>TF Setup</console-out>
  <console-error />
  </set-up>
  <counter duration="0" run-count="2" success-count="2"
failure-count="0" ignore-count="0" skip-count="0" assert-count="0" />
  <description />
- <runs>
- <run name="Tests.SetUp.CTTest(GetSomeTestItems(s1))" result="success"
assert-count="0" duration="0" memory="8192">
  <invokers />
  <warnings />
  <asserts />
  <Description />
  <console-out>Setup Test s1</console-out>
  <console-error />
  </run>
- <run name="Tests.SetUp.CTTest(GetSomeTestItems(s2))" result="success"
assert-count="0" duration="0" memory="0">
  <invokers />
  <warnings />
  <asserts />
  <Description />
  <console-out>Setup Test s2</console-out>
  <console-error />
  </run>
  </runs>
  </fixture>
  </fixtures>
  </namespace>
  </namespaces>
  </assembly>
  </assemblies>
  </report-result>


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