When you insert the Grooveshifter plug-in on a track, it causes the track's initial audio transient to fade in over a period of a second or so, rather than play with its normal attack. Playback is normal from that point onward, even when cycling.
This happens because Grooveshifter needs to be "primed" with audio before it can play, which causes the initial bit of audio fade in. You can compensate for this by choosing File > Song Settings > Audio, then turning on "Playback Pre-roll." With Playback Pre-roll enabled, the initial audio transient played through the Grooveshifter plug-in will be preserved.