ASP.Net: file or dependency not found, even though the site works locally, and I do not want it included in my solution?

I am publishing an Intranet on a VM for a company. The solution is made of 3 projects:

• StoxIntranet
• IntranetBaseClient
• StoxIntranet.Shared

Both Intranet and IntranetSupport have a reference pointing to the .Shared project, but neither have a reference to each other, and neither does the .Shared project have a reference pointing to the 2 side projects.

I tested the Intranet locally, and it works perfectly. However, when I publish the website to my VM's IIS, I am getting the following error, with this Fusion stack trace.

Could not load file or assembly 'Intranet' or one of its dependencies. The system cannot find the file specified.

=== Pre-bind state information ===
LOG: DisplayName = StoxIntranet
 (Partial)
WRN: Partial binding information was supplied for an assembly:
WRN: Assembly Name: StoxIntranet | Domain ID: 2
WRN: A partial bind occurs when only part of the assembly display name is provided.
WRN: This might result in the binder loading an incorrect assembly.
WRN: It is recommended to provide a fully specified textual identity for the assembly,
WRN: that consists of the simple name, version, culture, and public key token.
WRN: See whitepaper http://go.microsoft.com/fwlink/?LinkId=109270 for more information and common solutions to this issue.
LOG: Appbase = file:///C:/inetpub/IntranetBaseClient/
LOG: Initial PrivatePath = C:\inetpub\IntranetBaseClient\bin
Calling assembly : EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089.
===
LOG: This bind starts in default load context.
LOG: Using application configuration file: C:\inetpub\IntranetBaseClient\web.config
LOG: Using host configuration file: C:\Windows\Microsoft.NET\Framework64\v4.0.30319\aspnet.config
LOG: Using machine configuration file from C:\Windows\Microsoft.NET\Framework64\v4.0.30319\config\machine.config.
LOG: Policy not being applied to reference at this time (private, custom, partial, or location-based assembly bind).
LOG: The same bind was seen before, and was failed with hr = 0x80070002.

Why is this happening only when I publish the website, and where can I go remove this dependency, as I don't want IntranetBaseClient to have a reference to StoxIntranet at all?