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Got a malware on my hosting provider which infect JavaScript files .. how do I find the entry point?

This morning some sites which are hosted on the server as me started triggering malware alerts and started to redirect traffic to external sites. I've found out that a line of packed javascript was ...
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Javascript works everywhere else, except new server

Server A: Windows Server 2008 R2, IIS 7, admin - me Server B: Windows Server 2008 R2, IIS 7, admin - company server admin group I have a Javascript file that works well on my local machine. The JS ...