Well I'm not sure about Cakewalk Guitar Studio but I suspect it's like any midi sequencer but with guitar based notation and editing features and that sounds great.

Yamaha manual's are notoriously rubbish for getting the most out of your instrument.

try experimenting with the tempo, slowing it down to half speed.

put your 7 notes in and bare in mind the duration of each note. now play and see if it's the same problem even at this speed.

Ok now adjust the tempo back to normal speed, say 120bpm (beats per minute) and play again and see if that works.

Quantization is something to look into maybe..

Sorry no real answers there..