Justin,
I believe you are correct and I have indeed encountered DLL hell.
The DLLs being used are custom code I developed alongside the Outsystems extension. After reading more about DLL hell, I think that some refactoring that I did, after first publishing the extension and using it on the Outsystems module, such as changing the assembly, namespaces or class names, is the reason for this problem.
Even though I am uploading the correct DLLs in Integration Studio, the Outsystems application has been unable load the correct DLL and is trying to use the old one (which has different assembly and namespaces) hence the error on my initial post. This explains why the extension works correctly for a new Outsystems module, which does not contain older DLLs.
Now, is there a way to clear the older DLLs and force the new one to be used?
Regards,
João Mateus