When we link a Revit model into another project file there are number of instances where the linked model seems to interfere with selecting elements that are actually native parts of the model. I encounter this the most when I'm working with Revit MEP.
For example, using the Create System option for an Air Terminal the option to Select Equipment seems to only have eyes for the architectural model and it can be nearly impossible to select the very nice Single Duct VAV box right in front of you.
What to do? Well you could write a blog post like this and complain to start 8-).
If you change your view to Model Graphics Style: Wireframe you'll find that Revit is no longer as focused on the linked model. Another solution is to have a view with the linked model and another where the link is not displayed. When you are ready to create your systems just switch to the other "cleaner" view and no such issue.