I usually assume its 32 bit Java.
I develop on 32 bit Java. The heap settings are heavily tuned so if they revert to the JVM defaults then there will be the issue described... especially if it happens even while sitting still and not even looking around (animations pause for 30 seconds, etc.).
If it happens only when looking around and not while moving (Say, you were facing east and then turn to face west and get a long hang) then it's something else.
But regular long pauses no matter what are almost invariably Java performing a full garbage collection sweep because it was running out available heap memory. Most likely cause is that the memory settings aren't right... and at some point I added it so that the HUD shows the max memory in red if it was not what I expected. (Which signals false positive on 64 bit Java.)
