I have four projects in my Visual Studio solution (everyone targeting .NET 3.5) - for my problem only these two are important:
The issue I was facing was I have a project that is dependent on a library project. In order to build I was following these steps:
msbuild.exe myproject.vbproj /T:Rebuild
msbuild.exe myproject.vbproj /T:Package
That of course meant I was missing my library's dll files in bin and most importantly in the package zip file. I found this works perfectly:
msbuild.exe myproject.vbproj /T:Rebuild;Package
I have no idea why this work or why it didn't in the first place. But hope that helps.