Gatekeeper settings--app damaged

I made the mistake of listening to other Mac users when I wanted to get wifi who told me I didn't need to pay for an airport product. So I bought a Linksys router. After having a Panic yesterday I was advised to make sure my software & OS was up to date (there was a firmware update for my MacBookPro which I quickly & easily took care of) & also to update router firmware.
In the process of trying to do this, I discovered that the previous version of Cisco Connect software showed unsupported OS when I tried to open it. So needed to update. Finally found a link that was suposed to be for a Mountain Lion compatible update.
I downloaded it & then tried to open Set Up I would get a warning saying it was damaged but then help said modified or damaged.
But there was also a link there that I just clicked on Protect your Mac from malware & it talks about the Gatekeeper preferences.
For the setting Identified Developers which seems to be the default, part of it says:
OS X checks the app before it opens the first time to be certain it hasn’t been modified since the developer shipped it.
Just wondering how that applies to updates? I keep getting this same message, but I'm wondering, since it is an update of an earlier version whether maybe that is triggering the warning rather than something really being wrong w the software?
I have downloaded it 3x & I keep getting this same message so I don't know if the software is really faulty or if maybe Gatekeeper isn't recognizing it as an update or what.
The previous version that was installed, I suppose I could have updated to a compatible version if I had realized it needed to be done before upgrading from Snow Leopard to Mountain Lion. Also while Mountain Lion found Parallels 5 as incompatible, it didn't identify Cisco Connect as incompatibile w Mountain Lion.
I think I'm going to give up on the Linksys router. Their website wasn't very helpful & it has taken hours of my time just trying to get this part of it done & then I was going to upgrade the firmware which it warned could permanently damage the router if the update was interrupted. So I was going to download it 1st & then install from download--after I found it since I have intermittent loss of connection all the time.
But w all this, wondering again about the Gatekeeper functions whether this software really was damaged or whether there was a malicious or dangerous or corrupted change or whether it just didn't comply w Gatekeeper requirements?
So how do you tell about this & what to do about it? I mean the original warning sounded like it was all about it being damaged, but then as I read further it coudl also be that it has been changed since it was signed or whatever.
Seems like this could use some tweaking since there is a difference between software being damaged maybe during a download that I suppose could happen even from a trusted vendor vs potentially malicious software.
The way it is now, its not very Mac like--I expect Mac software to not raise questions that the average mac user doesn't understand & this does seem to do that.

Go to the spotlight search and type in settings, then you'll need to click on that then go to general and then reset home scren layout, so it will come back to your home screen.
Or you can double check your apps folder and see if its in there.

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