Your code doesn't seem to test what the author is discussing -- namely, after your assignment $B[5][2] = $A[1][1], does changing $A[1][1] change $B[5][2]? (Indeed, the only 'entangled' elements of your code are $B[5][2] and $A[1][1], and they aren't logged at the end.) With your choice of indexing, I think that what you want is:

perl -e '$A[1][1] = 33; $B[5][2] = $A[1][1]; $A[1][1] = 9; print "A = 
+$A[1][1], B = $B[5][2]\n";'
[download]

This prints out

A = 9, B = 33
[download]

which is exactly what (I think) you meant, and which certainly seems to be the behaviour desired by the original poster.

UPDATED (twice) -- I flipped the values of A and B (though I could have sworn I'd cut-and-pasted from the shell), and fixed a mark-up error.