Attempting to set two multi-configuration projects in sequence is problematic.
Steps to reproduce:
Create two multi-configuration projects (e.g. "foo" and "bar"), and configure
each one to build on two (or more) nodes. Go into bar's configuration and
attempt to put foo upstream (i.e. put "foo" in "Build after other projects are
built"). Save the configuration. Observe that the change did not take; bar has
no upstream projects.
Now, go into foo's configuration and put bar downstream (i.e. put "bar" in
"Build other projects"). Save the configuration. (This part works.) Go into
bar's configuration again, and note that "Build after other projects are built"
correctly lists "foo". Don't change anything, just save the configuration.
Observe that bar has no upstream projects again.
Two symptoms, but they definitely appear to be the same issue. The first one is
easier to work around, the second one is more of a pain. I first observed this
with (I think) v1.289, but I can't say for sure that's when it appeared. It's
still an issue as of v1.300.