I read some WhichAmiga changelog and found out the reason why such weird results were returned by 1.3.3:
Before kickstart 2.0, "extra" memory allocated by hunk alloc wasn't zeroed by LoadSeg.
I use this extra alloc space for variables, and didn't realize the memory might not be all zeros with Kickstart 1.x. The result was that various flags and variables would be set, and this explains the quite funky random output.