Hi All,
I contacted Emsisoft support and here is what they replied.
"Thank you for contacting our support.
Emsisoft Anti-Malware/Emsisoft Internet Security offers realtime protection and it detects malware right before it would want to execute and prevent it from doing so - this way no malware can harm your computer. So an USB stick is not scanned when you plug it in, but it is not possible that malware come to your computer as Emsisoft Anti-Malware/Emsisoft Internet Security would detect the malware if it would try to write itself to your computer. If you scan an external drive of course also latent/disabled/inactive malware on it will be found.
Thank you for using our software solutions! Should you have any further questions, please do not hesitate to contact me again.
Best regards,
Thomas Ott
Customer Support"
Seems like as the Viruses was Inactive that's why Emsisoft did nothing with realtime protection. Though it's ok now but realtime protection should detect the Autorun.inf file atleast.