I'm not sure how much of an issue its going to be, the concept is good, but here are a few comments:
1- Try and find a way to use something other than the windows pop-up (talk to the windows blind team or something). Make your icon jump 'a la MAC' or blink, but the windows tray pop-up has many negative connotations in people's mind and you may get inadvertently caught doing a good thing via a bad medium (the medium is the message or some crap like that....).
2- For future options that you introduce, make it clear you're introducing something and turning it on. I applaud the option to opt out (and honestly if you had done anything less Stardock wouldn't be the company I know it to be), but you should have shown this new feature prior to the impulse upgrade. I know I don't really have a choice and I have to upgrade Impulse, but do me the courtesy of letting me know what you're doing to my system. You have transparency as a key tenet of your company's modus operandi, don't lose it here; its one of the many things that take Stardock from a good company to a great one.
3- I have to put it twice, change the look of the pop-up window to something other than default windows pop-up. It is FAR TO reminiscent of SPAM, bad Tray viruses, and generally ugly stuff. It invites suspicion of your product just because of what others do with it; don't get caught up in it, move beyond it. I know your windows UI guys can fix this somehow.
Cheers,
Thanatos.