In our build process we were using the IDE from the command line to build the solution with the /Deploy switch to deploy BizTalk assemblies to BizTalk. This was ok locally, but when we wanted to export the MSI to deploy to other environments the msi would install the BizTalk assemblies to the paths you had used during development. This didnt really break anything but the resulting deployment was just messy.
To build your solution in MsBuild when it contains BizTalk projects you need to call the IDE from the command line, but when you deploy the artifacts to BizTalk it is better to use BTSTask and add them as a resource. This technique allows you control over the output paths when you produce the msi.
Another thing I did wrong was the first time I added them as an assembly. When i looked in BizTalk i couldnt see any of the schemas or maps etc. Remember to add BizTalk projects as a BizTalkAssembly for the resource type rather than a normal assembly.