Ok. It doesn't always happen to me, but I am using eclipse Luna on Ubuntu 14.04.
I noticed it personally while testing magic method injection, but it has also happened at work with a standard 2.7 SDK.
What I noticed is when I have a lot of files open, even if I am editing another file in a project not included in GWT, it is marked stale.
I know this because I added a bunch of debugging logs while working on magic method injection, and noticed the timestamp updates.
A co-worker has also reported the same issue with running full builds on a unit cache.
So, it's not in SDM in particular, it's in MinimalRebuildCache (which looks only at timestamps).
Once you can get enough files open that eclipse decides to touch your GWT files when saving other files,
then a rebuild always happens. Then I close eclipse, and it stops happening.
With my debug logging, and eclipse open, editing a file that is included, a bunch of other files were marked stale.
With eclipse closed, editing the same file, and only that file was marked stale.
I don't have a 100% reliable set of reproduction steps, but I have seen it on different machines using different builds >= 2.7