A couple of thoughts. Maybe the "Zero Controllers at stop" might have something to do with it. I know your clip is not technically "stopping" but maybe the resetting of controllers is what's causing SONAR to hiccup. Try turning it off temporarily and see what happens.
Also, you say the first beat is exactly on zero... maybe try moving that first beat a couple of milliseconds later than zero... I know your problem seems to be at the end of the loop, but it may be that the read ahead to go back to the beginning is effected by this.
Good Luck,
Rob