from the in-program help file:

"Be aware that using non-in-place plug-ins (such as Time Stretch, Pitch-Shift without preserving duration, and some Vibrato settings) will cause audio to play out of synchronization with the waveform display in the timeline and with other tracks. If an effects chain includes non-in-place plug-ins, the effects chain icon will be displayed as a [Pic of Yellow plug-in button]"

So, if you put a pitch effect plugin to slow down the audio, it will slow down the playback of the audio on that track, but this will not be reflected visual on the event waveforms. The yellow is a kind of warning that something of this nature is going on.