Some files are distorted at the very end when played with vgmstream resulting in an audible 'click' during the final frames.
Various versions of vgmstream were tested including the latest (r489). Conversions with Winamp & the test converter give the same results.
In all cases these files played flawlessly with in_cube.
Below two Gamecube games I've noticed to suffer from this with example files:
Metroid Prime 2 Echoes (PAL):
itm_x_short_00.dsp
itm_x_long_00.dsp
skytenkey-jin32.dsp
Paper Mario 2 (US):
evt_ed4_32k.dsp
ff_kpa2_32k.dsp
sys_demo2_32k.dsp