Some - Not All - Audio Apps Bypassing Sound Preferences Control

Hi folks.

I'm having issues with audio apps on my Mac. I'd appreciate any advice
from those who have personally witnessed and dealt with this.

I have a Power Mac G4/400 AGP on OS X 10.2.8 with an M-Audio Delta
Audiophile 2496 installed. All of the system software and AP2496 drivers
are latest currently available.

A couple of weeks ago, sound output from Web plug ins (Flash most
notably), QuickTime, Windows Media Player, RealOne player, iMovie,
MacAmp, and iChat stopped coming through Sound Preferences pane. I
cannot change the volume using the Sound Preferences pane controls, the
Menu Bar volume control, or with the AP2496 Control Panel. Only the
volume control on each application will control its own sound level. In
addition to having this problem with 100% of the audio content played by
the mentioned apps, I've also found that any media files played by
iTunes that require the use of another app's codecs to decode the file
(such as using QuickTime to play .MOV files) will not pass through Sound
Preferences pane.

However, output from iTunes (playing media that is decoded by iTunes's
internal codecs (such as MP3 (both CBR and VBR), Audible, and M4P),
SparkME, Sound Studio, Amadeus, and the OS X DVD player can be
controlled by Sound Preferences pane, allowing me to not only direct
output to either internal audio ports or those of the AP2496, but to
control the sound levels using all appropriate level controls.

The System Alerts controls are unaffected; can be directed through to
the internal ports or the AP2496, as well as levels being controlled, at
will.

I have deleted, cleaned out, and reinstalled all affected software. I
have deleted plists to no avail. This erratic behavior continues. The
only thing I can think of is that my very brief evaluating of either
Jack OS X or WireTap at the time may have caused this, but I have been
unable to find any residual artifacts left behind after a
seek-and-destroy mission as a superuser to remove them.

Anyone have any ideas? The only piece of software I haven't deleted and
reinstalled is Sound Manager and/or the Sound Preference pane itself.
Will this work, and if so, how do I go about reinstalling those without
reinstalling the entire OS?

Thanks in advance.