We have found a solution : the issue was the \n character (maybe a change with the SPL in the v6.5 ) in some of our alerts.
Please find below the answer of splunk support on this :
"We have a few related sounding known issues like this (listed below).
Your one actually isn't documented externally yet though.
Internal reference (which you can us when talking to support/accounts team is SPL-129846). It is a regression bug, and is due to be fixed in 6.5.1.
http://docs.splunk.com/Documentation/Splunk/6.5.0/ReleaseNotes/KnownIssues
SPL-34347 = wmi input default fields - with value including newlines doesn't search properly becasue of \r\n issue
SPL-74209, SPL-74167 = Persistent queues are not created on Windows for stanzas that contain unusual characters (such as < and >).
Workaround: Specify the persistentQueue explicitly in the input definition.
SPL-78179 = REST /saved/searches App names with special characters have invalid links. "
