I'm not exactly sure what's causing it. Something such as SCC vs SCC+ differences should be causing total failure on improper implementation, not this.
VGZ/VGM don't play with foobar2000 1.01.
I hear a tiny crackle when switching between SPC tracks. It may happen with other formats, but the SPCs are the most obvious.
Also, why exclude SPCs from the sample rate selection? I know 32000 Hz is native, but so is Gaussian interpolation.