Visual Studio 2013 deploying incorrectly the content types of a document library

Question

Hello everyone. 
I created a SharePoint farm solution in VS 2013. I add four content types (say, C1, C2, C3, C4, based on the Document content type) and I create a couple of document libraries (say, L1, L2). Now I add C1 and C2 to L1, and add C3 and C4 to L2. 
When I deploy the solution from VS, I go to the site and found out that L1 has C1 and C2, as expected. However, L2 has C1 and C2 instead of C3 and C4. 
I have reviewed for hours the xml files (Elements, Schema, etc.) and all IDs seem to be correct and all properties are in order. 
Has anyone come across a problem like this? Any thoughts will be really appreciated, as I'm clueless and frustrated at this point, after hours of dealing with this problem. 
Thanks in advance!
Best regards
Fernando A. Gómez F.
fermasmas.wordpress.com
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Answer 1

Hi Sohel, thanks for your reply. 
No, I don't add them programmatically, I added the "Content Type" and "List" items to the VS solution. It generated some files, including Elements.xml and Schema.xml. Then I used the integrated VS designers to add the content types to
the list. A very run-of-the-mill solution, I think, nothing too fancy. 
One thing I noticed is that I created a feature, and everytime I add a new list, instead of using the existing feature, it creates a new one, which I delete, and then add the list to the existing feature using the designer. 
Finally, something weird happened today. I opened my VS, opened the solution and there was several feature files created out of the blue by the VS. I thought something was messed up with the Visual Studio Online connection, but it happens anyway when working
in disconnected mode. 
Fernando A. Gómez F.
fermasmas.wordpress.com
Galería de ejemplos