Hi Jan,
I think I found the problem. In the SD_DQEReferenceXmlIncludeTemplate(dqeReferenceXmlInclude.template):
<Reference Include="SD.LLBLGen.Pro.DQE.SqlServer.NET20, Version=3.1.0.0, Culture=neutral, PublicKeyToken=ca73b74ba4e3ff27, processorArchitecture=MSIL">
<SpecificVersion>True</SpecificVersion>
<HintPath><[RuntimeLibraryHintPath20]></HintPath>
</Reference>
It should say: Version=3.5.0.0. This template is specific for each database.
We are looking into this. In the meantime please fix the reference manually.