I have had a problem forever with the volume of the Mac being too low with some applications.
The Mac is a sawtooth running OS 10.2.8
The start up chime volume is very loud when I have the volume at full level; the alert tones aren't quite as loud, but still very audible.
But when I play certain video clips, using a flash player just now, the volume is barely audible even at maximum level.
I have looked high and low on the Mac wondering if there is a secondary volume control that I can increase, but no luck.
I have cranked up every volume control I can find, and the level is still in the mud, typically for flash palyer clips.
Downloaded the latest flash player today, still the same problems.
One solution is to plug in external speakers - I may have to do this again - just don't have any more room on my desk.
One thing you might try is making sure that your Audio Midi Setup (Applications/Utilities) is configured properly. If I remember correctly, at one point there was an issue with it. Not sure if it's the root of your problem.. however, it may just help.
Make sure the "Format" for your Audio Output is 44100.0 Hz and 2ch-16bit.
Not sure if the link gets you to the video directly.
Even with the volume at maximum I can barely make out some of the words the actors are saying.
And yes, I do repair permissions regularly.
Like I said, if I restart my Mac now with the volume way up I get a super loud start up sound, so the volume issue is somehow related to the application or the actual file.
The volume of the ad at the beginning is low but still clearly understandable. In the actual clip you have to be close to the speaker to hear some of the words (shouldn't be like that at max volume). Probably doesn't help that my Mac is underneath the table, but still - the difference in volume between the alert sounds and this audio is huge.