Okay, I see what you're doing wrong.
You are trying to create a three-measure groove clip. That's 12 beats.
When Sonar estimates the clip length, it will typically "guesstimate" to 2, 4, 8, or 16 measures - whichever is closest - as these are the most common loop lengths used in dance music. Since you said it's "larger," then I assume Sonar guessed the 12-beat clip was 16 beats.
When I duplicated your steps above, Sonar generated a groove clip that was 16 beats. In the loop construction window, "Beats" said "16." I changed it to "12," because you specified you had created a clip with 12 beats.
As soon as I did that, the groove clip was 3 measures (12 beats) long and did exactly what you wanted it to do.
Groove Clips are NOT broken, but for situations outside the normal 2-4-8-16 loop lengths of dance music, you will almost certainly need to tell Sonar the number of beats. I did several loops once in 7/8 and believe me, Sonar did not guess those right, either.
P.S. This isn't a diss on tech support at all, I've probably logged more hours in the Loop Construction window than ANYONE at Cakewalk...maybe anyone on the planet...
P.P.S. I'm determined to fix this for you so please provide all pertinent information - e.g., what the "Beats" parameter says in the loop construction window.
P.P.P.S. One reason why the acidization is so lousy in loop libraries is that they just put the loop into Sonar or Acid, click on "make this friggin;' thing a loop," then think that the loop is therefore acidified. No!! Except for all but the simplest loop, Acidization (or groove-clip looping) will require some tweaking and manual intervention. This is also true with Apple Loops and REX files, so you won't get any relief there either.