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At a guess, you have more than one sound output device set up, and different programs are accessing different devices.
You don't say which distribution you are using, so I can't give you accurate information on how to set up your sound devices. If you are using Ubuntu then there should be a volume control icon on the panel (or you can right-click to add it). If you right-click on that and select "open volume control" then you can select the volume for the various devices that you might have.
Note that some devices are software devices created for compatibility with other programs.
Firefox has no sound settings because it doesn't access the sound drivers itself; you will need to look at the settings for flash player itself (which can be configured by right-clicking on any flash object).
Another possibility is that some programs are using real OSS for sound, which will only allow one program to output sound at a time. You can get around this by installing the OSS compatibility layer for ALSA, usually a package named alsa-oss or similar in your distribution's package manager. This replaces your OSS devices with software devices that pipe sound through ALSA, which can mix sounds from different sources.
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