If I click Practice then click on Study next to the book I'm studying (Remembering the Hanzi 1) I am presented with the normal character pad however after drawing the character I am not given a chance to select the tone I think it is. This only happens when I follow this path to the character pad. I don't have this problem studying from my own custom lists for example.

The tone probably wasn't due for that character, so it wasn't prompted. We don't ask the tone every time if you know the tone better than the character, and vice versa. Could that explain it?

I guess so; I suppose the problem lied in my what my expectations were when checking off that 'Tone' box. In general, I wish that there was some way to put Skritter into 'manual' mode for those times I wish to exercise greater control (this would extend to character scheduling, etc.).