Thanks for the bug report and apologies for taking so long to respond. This is fixed in version
1.13, released 2012-09-02, now wending it's way into CPAN.
The problem was actually in the superclass Hash::AutoHash which was overriding 'isa' (along
with 'can', 'DOES' and 'VERSION') in an overly ambitious attempt to permit all syntactically valid
methods to be used as accessors. This worked until Perl 5.9.3 deprecated the use of
UNIVERSAL methods as functions and recommended that developers use method form instead.
Test-Deep-0.109 took this recommendation to heart and invoked 'isa' on references to decide
if they were 'special test tokens'.
All the best,
Nat