You should be mindful of gestalt principals when grouping or aligning controls.
Gestalt principal of perception states that when looking at a complex visual image, our minds see coherent, whole forms, rather than individually perceiving all of the smaller elements in the image.
For grouping controls, alignment will of course make a form more pleasing to the eye, but take care that you get the spacing right or the user will see "groups" of controls that you did not intend.
The above image illustrates what I mean in relation to your question. In the first example the alignment combined with inadequate spacing forces the user to see the controls from 2 different groups as being a single entity. In the second example all the controls are still aligned, but now the spacing aids the user in seeing them as 2 seperate groups.