This can be re-produced with multi-module maven project as sub-module's configuration is usually pretty short (depending on installed plugins) and it thus fits entirely on one browser page.

1. Select a multi-module maven project.
2. Click Modules on the left bar.
3. Select a sub module.
4. Click Configure on the left bar. Save button is nicely below the settings (initial.png).
5. Click E-mail Notification tick box (email_clicked.png) or its help button (email_help.png). In both cases Save button stays in place and hides some of the page content.
6. Expand helps (those question marks at the right end of the page) such that configuration page no longer fits on one screen (vertical scroll bar becomes available). The Save button is nicely positioned at the bottom of the screen when scrolling up and down. Page content is not hidden.
7. Collapse helps. Save button is found at the bottom of the page (button_at_bottom.png).

Save button can be returned back to its correct place if browser window is re-sized, or Find... (ctrl+f) is selected.