Definitely not the same problem then. Fortunately there are always different options around including Schibo's (1964 only AFAIK) and Azimer's older .40 beta 2. Also try a different emulator- if you're using PJ64 try 1964. If you are using 1964, that may be your problem anyway since someone mentioned the Azimer .55 currently works properly only with the audiofix version of PJ64 he released with the plugin. Or is it .50 beta 2 you're using? Anyway, my point is fool around with different emulators and plugins. One of them is bound to work better for you.
EDIT: I just tried the 0.50 beta 2 plugin myself and I get this jamming problem you describe playing Zelda:MM. On the Audiofix version of PJ64 (yeah I know, it's designed to work with 0.55 Alpha not 0.50 beta 2) when the sound first came on as the mask flies toward the screen and back it jammed as you described it right away. I decided to try it in PJ64 1.51 and it jammed after a save state. My recommendation is definitely to try a different plugin as this is the only one that gave me this problem. My specs? 1.1GHz Athlon, SB Live Gamer sound, Win XP, 384MB RAM, using Glide64 0.70ME w/eVoodoo 3.99 on a Radeon 7500 (64MB).