This thread makes my head explode because I just don't get exactly what you're trying to accomplish...creating grooves with silence (although no audio input doesn't mean there's silence; there's still preamp noise etc.), and making really long grooves to roll them out. If you have something like a 96 measure clip, at usual tempos that's over a minute...seems if you just copy a couple more instances you'll have several minutes of audio?
Groove clips are designed to create, well, groove clips. These tend to be relatively short, repetitive patterns. I use this feature all the time and never encounter any issues, as long as snap to zero audio crossing is off. The worst thing that happens is if Sonar guesses my intentions incorrectly, and doubles the number of beats. But that's easy to fix by entering the number of beats.
If you're trying to accomplish a particular function by using a function in a way it wasn't really intended to be used, it's generally best to find a different way to accomplish that function using a workflow that's more congruent with the intention of the function.
But maybe I'm missing something...like I said, this thread makes my head explode!