How to reproduce:
1. Create a Unity project (with 5.5.0f3, for example) and close it
2. Open it with 5.5.2p1 and close it (make sure, you do not save the project)
3. Open it with 5.5.2p1 again

Expected result: No warning message is shown, because the project has already been opened in a 5.5.2p1 version
Actual result: Warning message "Your project was last opened with a diffrent setup of Unity..." is shown

Reproducible with - 2017.1.0a2, 5.6.0f3, 5.6.0b10, 5.5.2p1
Not reproducible with - 5.4.4p2

Notes: Not reproducible when loading project on newer major version, for example, going from 5.5 to 5.6, or from 5.5 to 2017.1