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Thank you for your help. I have found the issue by excessive google search here: https://kb.fortinet.com/kb/documentLink.do?externalID=FD52723
There is a seperate latency option for maximum acceptable latency before the fortifgate considers the packet as lost. set probe-timeout
The default value is only 500ms so even if wireshark reports no packet loss fortigate says if icmp response time > 500 ms then consider as loss. I have changed the value now to 5000 ms its max value and now it seems to work.
