Just an update that may be useful for users that want to temporarily fix situation.
Looking into plutomedia mysql tables I've found how to settle private media visibility.
Making it short, it is enough to perform the following SQL statement:
UPDATE `File` SET `FK_MediaSubType` = NULL ,
`FK_FileFormat` = NULL ,
`EK_Users_Private` = 'your userID',
`EK_Device` = NULL ,
`psc_id` = NULL ,
`psc_batch` = NULL ,
`psc_user` = NULL ,
`psc_mod` = NOW( ) ,
`psc_restrict` = NULL WHERE `Path` LIKE '/path/to/your/private/media'
AND `EK_Users_Private` IS NULL
This will set the proper value into EK_Users_Private, making the related media somehow private to the specific user.
This confirms that most probably the last version of UpdateMedia does not set properly the named field (atually it leaves it as NULL), so that all media are considered public.