Alert volumes not adjusting when I make changes

I've been using Sound Bunny to control volume levels in different applications for awhile now in OS X 10.7. I just moved to a new Mac Pro, however, and now that my OS is 10.8.3 I'm getting certain apps greyed out because they are sandboxed. It's annoying to be sure, but I figure, "that's alright, I'll just adjust the alert volume level in System Preferences." No such luck.

I've changed the alert volume levels, chosen different sound files (trying to choose some that are quieter) but all my alerts, especially those for Mail, are coming through at full volume. They're really loud and dominate everything, half scaring the life out of me because of the volume level. So now it seems that not only can't I adjust the volumes in Sound Bunny (some of the apps that utilize alerts the most are unavailable now - sandboxing *****), but I can't adjust them in System Preferences either.

I've been using Macs for 15 years now, so I like to think I know most simple tricks or fixes, but I always find myself in the wrong, haha. There's always some new issue that I'm in the dark on, and I'm completely stuck on this one. I've googled the issue and haven't found anything, nor did I find any topics here that seem to address this.

Any help would be greatly appreciated.