Aquaria checks for a file named "ran" in its directory. If AQConfig didn't crash on you, it should have generated the file. However, if it doesn't have permission to do so from the OS, then it can't make the file. If Aquaria doesn't find the file, it'll just loop you back to AQConfig. So run AQConfig as admin (right click on it and click on "Run as Administrator").
If that still doesn't work, manually create the file. Open a text editor (such as WordPad or NotePad) as admin, and then enter a few digits in it (mine says 97). Then save the file under Aquaria's directory with the name "ran". You may have to rename it if your text editor saved it as a .txt.