When %appdata% is an UNC share path, all user options will not be saved in %appdata%\Roaming\LibreOffice\3\user\registrymodifications.xsu. Version 3.4 works fine. Version 3.5 has the same problem.
(Can not reproduce with a quick check of current master on a Windows 7 VM, pointing UserInstallation at file://vboxsrv/share/USER on a vbox-provided volume shared with the Linux host.)
We use 4 Terminal Server Windows 2008R2. Our %APPDATA% directory points to a file server by UNC path. Our windows envoirment variable contains "APPDATA=\\fileserver\FOLDERR$\FOLDERR\username\AppData\Roaming". All user options normally will be saved in "%appdata%\LibreOffice\3\user\registrymodifications.xcu". In Version 3.4 all works fine. In Version 3.5 and Version 3.6 the file will not be updated when the user makes option changes.
Do not hesitate to reopen in case of mistriage. *** This bug has been marked as a duplicate of bug 50542 ***