Weird one of those "allow" pop-up for less than a second, keeps coming up periodically....what is this?!

I am getting a weird pop up, it happens after i log in and then periodically as i am on my computer. Not at any time in particular, happens as I am surfing the web or using applications like iphoto. Its one of the pop ups that would come up to allow something, but its only up for maybe half a second, i can just make out the yellow caution sign that shows up on the allow pop ups for things. I tried downloading a virus software for mac and checking for viruses but couldnt find any. A bit stumped as to what this could be?
Any suggestions or thoughts are appreciated.

Yes it occurs when I am not using a browser, although I am not sure entirely if safari was quit or not however it has occured even when I don't have one open
I only have the one account, I just put the login on because I won't be using my computer all summer. So other than the guest account there is just my main one, and from what I remember it began happening before I did this
I have not tried booting in safe mode...although it would be hard to tell because I never know when it is going to pop up

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