Like the topic states: Upgraded but version is not updated.
How to reproduce:
0. First I've emptied the core/cache/*
1. wget https://modx.com/download/direct?id=modx-2.5.4-pl.zip
2. unzip direct?id=modx-2.5.4-pl.zip
3. cp -rf modx-2.5.4-pl/* . (I'm in web root folder)
4. https://mysite/setup
5. choose upgrade
6. no warnings, no errors
7. deleted setup folder and logged in;
8. version still shows 2.5.2
9. Emptied browser cache, but no change!