How to deal with assembly and DLLs in DLL hell?

Question

I am working on two DLLs, being called by an application. Everything is programmed in C#.
Recently I've tried to work with pre-build events, in order to add some versioning information to the DLLs. I have removed all that work: in GIT, all files (project files, source files, AssemblyInfo.cs) are present in GIT and there are all changes are deleted. There are just some leftovers (like FixedAssemblyInfo.cs files and AssemblyInfo_Orig.cs), but those are not referred to in the project files.

In order to work with the DLLs, I build them into a Modules directory and I use Application_Server.exe as an external program for running the DLL. That application is the same for both DLLs.

When I try to work with DLL1, everything is working fine.
When I try to work with DLL2, I have the following weird error message:

Source code (source_file.cs):

using System.Xml;
using System.Xml.Serialization;
...
var serializer = new XmlSerializer(base.GetType());

Error message (Exception thrown):

System.IO.FileNotFoundException: 
'Could not load file or assembly 'Application_Server.XmlSerializers,
                                  Version=1.0.0.0, ...' or one of its dependencies. 
The system cannot find the file specified.'

Why is this strange?

1. source_file.cs belongs to DLL1, not to DLL2 (and I'm busy working with DLL2).
2. When I launch DLL1 (which launches the same external application as DLL2), everything is working fine.

Anybody has an idea why DLL2 does not want to refer to System.xml.dll, and this in a source file of DLL1 while that same DLL1 does not have that problem?

Thanks in advance

Edit: Process Explorer results:
I just ran Process Explorer (while debugging DLL2 in Visual Studio, having the Exception's error message open): apparently Application_Server.exe has System.XML.dll loaded.

Edit: callstack:
Hereby the (partial) callstack when the Exception occurs:

 mscorlib.dll!System.Reflection.RuntimeAssembly.nLoad(System.Reflection.AssemblyName fileName, string codeBase, System.Security.Policy.Evidence assemblySecurity, System.Reflection.RuntimeAssembly locationHint, ref System.Threading.StackCrawlMark stackMark, System.IntPtr pPrivHostBinder, bool throwOnFileNotFound, bool forIntrospection, bool suppressSecurityChecks) Line 1951    C#
 mscorlib.dll!System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(System.Reflection.AssemblyName assemblyRef, System.Security.Policy.Evidence assemblySecurity, System.Reflection.RuntimeAssembly reqAssembly, ref System.Threading.StackCrawlMark stackMark, System.IntPtr pPrivHostBinder, bool throwOnFileNotFound, bool forIntrospection, bool suppressSecurityChecks) Line 1859    C#
 mscorlib.dll!System.Reflection.Assembly.Load(System.Reflection.AssemblyName assemblyRef) Line 363    C#
 System.Xml.dll!System.Xml.Serialization.TempAssembly.LoadGeneratedAssembly(System.Type type, string defaultNamespace, out System.Xml.Serialization.XmlSerializerImplementation contract)    Unknown
 System.Xml.dll!System.Xml.Serialization.XmlSerializer.XmlSerializer(System.Type type, string defaultNamespace)    Unknown
 System.Xml.dll!System.Xml.Serialization.XmlSerializer.XmlSerializer(System.Type type)    Unknown
>Application_Server.dll!Application_Server.Communication.Messagess.Message.ToString() Line 123    C#

Edit: Project properties "Build" tabpage
My Project's "Build" properties page looks as follows (both for DLL1 and DLL2):

(As that modification does not solve the issue, I've decided to remove it.)

Important edit: modification of bad reference
In DLL1, there was a reference to an older version of DLL2. I have replaced that reference with a reference to the current DLL2 but that did not solve the issue (I've been checking the entries in the .FileListAbsolute.txt in order to be sure).