I recently upgraded CJT to the latest version (I've tried both 6.0.12 and 6.0.13) and noticed that the pagination of my main blog feed is then broken.
If I disable CJT, then it works properly again. I'm running WP 3.5.1 with GoodLayers 'Green Earth' v1.05. I initially posted the problem to their support forums, and they suggested disabling plugins and turning back on one-by-one, which is how I identified CJT. They haven't investigated further, but I wanted to make you aware of the conflict and see if you have any ideas. Thanks.