+1  A: 

Changing the target runtime will not change where your run configuration points.

You need to go into your Run/Debug configuration and change the execution environment there to point to the desired target.

Personally, I think this behaviour is confusing. I recommend filing a bug against Eclipse to make this easier to use.

Francis Upton
Could you clarify where exactly to change the Run/Debug configuration? The only Run configuration I see seems to be pointed to the correct runtime. I have attached screenshots to my original question.
Eric J.
Oh, actually I was answering a question thinking about the Java JRE instead of the target runtimes. I don't know for sure, but I think the target runtimes have the same issue. Your 2nd screenshot would be where you change it in the drop down list. Are you sure that changing the project preferences is having any effect on the run configuration? I would expect it not to. If it is changing it sometimes and not others, you should file a bug about this.
Francis Upton
A: 

The problem was that the POM file specified a name of SpringSource v1.0, while the Eclipse runtime environment only had a server defined with the name SpringSource dm Server (Runtime) - which is the default name suggested by Eclipse when creating the server.

Defining a server with a name of SpringSource v1.0, matching what is stated in the POM, resolved the issue.

Eric J.