In many systems, there is a way to convert audible alerts (e.g. a beep) to visual alerts (e.g. a brief flash of the screen). These can be configured on a per-application basis (e.g. .Xdefaults file, --visualbell option and so on) so check you don't have something like that in place.

From Perl, have you tried:

print "\a";
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You mentioned generating these sounds in response to certain events. There may be something related to the code monitoring these events which can do this. Without seeing any code, I can't be specific but, as an example, from Perl/Tk's event loop you can do this:

$widget->bell();
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