I think, the problem to show that two sequences are the same straightforwardly leads to the problem to find a presentation for the Rubik's cube group
http://en.wikipedia.org/wiki/Presentation_of_a_group
What we call "canonical sequences" is for example the group defined by the presentation
<U,R,F,D,L,B|U^4=R^4=F^4=D^4=L^4=B^4=U D U^3 D^3=R L R^3 L^3=F B F^3 B^3=1>
With the presentation given above we can for example formally show that U^2 D^2=D^2 U^2:
Because of U D U^3 D^3=1 we have U D U^3 D^3 D=D and because of D^4=1 we get U D U^3 = D.
Right multiplication with U gives U D = D U.
Now we have U^2 D^2 = U (U D) D = U (D U) D = (U D) (U D) = (D U) (D U) = D (U D) U = D (D U) U = D^2 U^2 q.e.d.
Of course we can *not* show with the presentation given above that for example D2 L2 R2 D2 U2 L2 R2 U2 = 1. So the presentation given above surely does not give the cube group. But we could add the relation D2 L2 R2 D2 U2 L2 R2 U2 = 1 to get a "better" group. The problem to find a presentation for the cube group is still unsolved.