aspnet_merge(0,0): Error occurred: An error occurred when merging assemblies: Unresolved assembly reference not allowed: [Custom.Assembly]

I'm a long time Stack Overflow lurker, and this is my first question so please go easy on me.

I develop custom eCommerce ASP.NET Web Forms applications, and during publishing we merge all outputs to a single assembly.

I've been scouring the web trying to resolve the below error during publishing:

aspnet_merge(0,0): Error occurred: An error occurred when merging assemblies: Unresolved assembly reference not allowed:[OurCustom.Assembly]

This has never been an issue with any of our other projects, and I'm totally stumped.

I have tried:

Checking out a clean project from our repo
Removing than re-referencing all .dll's in the bin folder
Using different versions of aspnet_merge
Switching target framework (.NET 4.5, 4.5.1, 4.5.2)
Turning computer off, then on again
Sleeping on it

The .dll in question is used in all of our other projects, and has not caused this issue before.

Thanks in advance.

Solution

After much trial and error I was able to determine that our custom .dll the project was referencing was corrupted, even though it worked locally and in production. I copied in another version of the .dll that worked with in the other projects and was able to publish to a merged assembly.