Update on this issue. It seems like the root cause for the Chrome issue is Symantec falsely detecting our program as risky/potentially dangerous. Which in itself is very strange given the fact that our digital certificate is issued by VeriSign and there haven't been any false positive issues with Symantec for very long. We assume that Chrome somehow uses the data from Symantec and aggregates them with data from other vendors, but we are not sure. We have already reported this to Symantec and hopefully the issue will be resolved soon.
It should be noted though that Google Chrome is very quick in going from a mere assumption to a final verdict. That is from the subtle "may harm your browsing experience" to calling the file as being outright malicious. :D
UPD: sorry, just noticed that you have already provided the instruction in your message. So I've deleted mine :)