There are seperate settings for out of holster and in-holster settings in Profiles. I guess that the original idea was that you could have a louder or even a different ringtone whilst the phone was holstered. Ancient BlackBerrys could not play MP3s (yes, I know that sounds strange) and had very quiet ringtones.
So go into Profiles, Advanced, select the Active Profile to edit, select a function to change and then scroll down to the lower part of the screen where you will find the In Holster settings.
This is from my 8900 but the Storm screen should be similar.