The JabRef installer 2.3.1 doesn't run as administrator, so it doesn't install into "C:\Program Files\JabRef" and instead attempts to install in e.g.
"C:\Users\[user]\AppData\Roaming\JabRef 2.3.1"
Version: jabref 2.3.1 November 29, 2007
Workaround: Right-click JabRef-2.3.1-Setup.exe and select "Run as administrator". This will then allow it to install correctly in "C:\Program Files\JabRef"
(Previously both the installer and executable triggered UAC, but the executable is fixed OK - see https://sourceforge.net/tracker/?func=detail&atid=600306&aid=1841602&group_id=92314.
But now the installer doesn't trigger UAC even though it probably should.)
NB: It is possible that this is desired behaviour to allow a non-administrator to install JabRef, but if this is the case the installation documentation should probably instruct administrators to run the installer as administrator to get the standard installation behaviour.