There's three volumes that affect your notification sound.
There's the main ringer volume, there's the notification volume, and then there's media volume.
-Try increasing your media volume by doing the following. Pick a notification sound from the list that is longer than most. Press it, as it begins to play the sample of the sound immediately start pressing the 'Up Volume' key. You should see it adjusting the Media Volume on your screen.
-From the same screen with the list of notifications, adjusting the volume buttons while a tone is not playing will adjust the Notification Volume.
-A third factor you may be experiencing has to do with some usually well implemented HTC speaker vooddoo between the rear speaker and earpiece speaker. I dont have time right now to go in depth on this, maybe in days ahead. But for now, maybe try removing any case or skin you have from the phone, then let the phone sit face up on a non-reflective flat suraface such as a non glass table. Then test your sounds and tones again. Might make a difference.