The problem shows when:
For some module A there is a mapping from module B to module B1.
Module A refers to module B by relative ID.

Test case:

define('lib/b', [], { message: 'B' });

define('b1', [], { message: 'B1' });

define('lib/a', ['./b'], function(B) { 
    return { message: 'A ' + B.message }
});

require({
    map: {
        'lib/a': {  
            'lib/b': 'b1'
        }   
    }
},['lib/a'], function(A) {
    console.log(A.message)
});

Expected: A B1
Actually: A B

It seems that problem is in normalize() function: in case relative module ID is used it removes from baseParts array last element, so apply map procedure doesn't check mapping for full baseName.