significant bug with Bio::LocatableSeq

While debugging some tests in bioperl, I noticed a fairly significant  
issue with Bio::LocatableSeq which is probably due to some  
inconsistencies with start/end coordinates.  For some reason this  
started popping up with error messages recently when running AlignIO  
tests on bioperl-live (i.e. something changed which exposed the bug,  
maybe the verbosity level):

1..295
ok 1 - use Bio::AlignIO;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6 - The object isa Bio::AlignIO

--------------------- WARNING ---------------------
MSG: In sequence 02 residue count gives end value 399.
Overriding value [355] with value 399 for Bio::LocatableSeq::end().
STACK Bio::LocatableSeq::end /Users/cjfields/bioperl/bioperl-live/blib/ 
lib/Bio/LocatableSeq.pm:150
STACK Bio::LocatableSeq::new /Users/cjfields/bioperl/bioperl-live/blib/ 
lib/Bio/LocatableSeq.pm:103
STACK Bio::AlignIO::arp::next_aln /Users/cjfields/bioperl/bioperl-live/ 
blib/lib/Bio/AlignIO/arp.pm:106
STACK toplevel t/AlignIO.t:34
---------------------------------------------------
.... followed by tons of similar errors.

The problem is, no change is ever made.  This is demonstrated by the  
following: