It seems that Seconds are ignored in formula fields if you create the difference between Datetime/Time fields.
Say you have two Datetime fields: End__c and Start__c
Take a formula field Duration__c (in Seconds) defined as
(End__c - Start__c) * 24 * 60 * 60
- End__c is "2014-08-31T18:52:40.000+0000"
- Start__c is "2014-08-31T18:52:38.000+0000"
Duration__c evaluates to 0.00 seconds but should be 2.00 seconds