I knew about the first click problem but to be honest I never found out why it happened.
The smooth warning is issued by Processing and I will have to double check I fixed that for the new version. At the moment simply ignore it.
Shapes3D V3 is well advanced and I am updating my website with new guides so please have a look and let me know what you think. The shape picking has been improved, it is more accurate, no longer misses the first click and informs the user which part of the shape has been clicked. So for a Box not only will you know it has been clicked but which face you clicked on.
Both V2 and V3 use a colour picking algorithm for shape selection. It creates an offscreen buffer on first use so there is a slight millisecond delay on first click. This is called lazy instantiation since the buffer is only created if needed.