Steps to reproduce:
1 create a new empty project
2 close the editor
3 change the content of ProjectSettings/ProjectVersion.txt to version 2017.1.0f3
4 open the editor (version 2017.1.1.f1) and observe the version of the project in the list of recent projects (2017.1.0)
5 open the project and accept project upgrade
6 close the editor
7 open the editor (version 2017.1.1.f1) and observe the version of the project in the list of recent projects (2017.1.0)

extra step: open ProjectSettings/ProjectVersion.txt and observe that it's not updated (2017.1.0f3)

Expected result:
project version upgraded in the list of recent projects after the upgrade
ProjectVersion.txt file updated with the version of the editor upgrading the project

Actual Result:
same project version in the list of recent projects
ProjectVersion.txt not updated with the correct editor version

It's not reproducible in version 5.4.6f1 and 2017.2.0b11
Reproduced in 5.6.2p4 and 2017.1.1f1

Workaround: set version manually in ProjectSettings/ProjectVersion.txt to the correct version to avoid project upgrade each opening