Tempo Matching audio

Probably should ask this in cubase forum but it may be a bug in Nuendo [although more likely user error].

I have a freely played guitar track in two parts; verse and chorus. I position them on the time line with the correct ‘musical’ distance between them. I make them one part so I can move them around. The track is in musical mode. I make the part start on the first beat of the bar and tap tempo a midi hi-hat track to them. I tweak all the hits, select them all and select ‘merge tempo from tapping’. The first bit of audio in the part is in time but not the second. I did try it with the audio not as one part and even on different tracks but to no avail.

Any ideas anyone? What am i doing wrong?