Not quite sure (I suspect it's a bug), but it seems like it has to do with the implementation of make-readtable (which brackets.scm uses).
$ mzscheme
Welcome to MzScheme v4.2.1 [3m], Copyright (c) 2004-2009 PLT Scheme Inc.
> (parameterize ((current-readtable #f)) (read))
x`y ; read in as two items
x
> y
> (parameterize ((current-readtable (make-readtable #f))) (read))
x`y ; read in as one symbol
|x`y|