> I expected to get the same results for these two \showbox commands.
Yes you should.
Consider the following (as long as the 8bit lines of latin-1 get
through the mail)
It produces four identical results, each looking like:
> \box0=
\hbox(8.56377+0.0)x27.21558
.\T1/cmr/m/n/10 ^^c1
.\kern-0.83313
.\T1/cmr/m/n/10 ^^dd
.\kern-0.83313
.\T1/cmr/m/n/10 ^^c1
.\kern-1.11084
.\T1/cmr/m/n/10 V
\documentclass{article}
\usepackage[latin1]{inputenc}
\usepackage[T1]{fontenc}
\showoutput
\setbox0=\hbox{\'A\'Y\'AV} \showbox0
\setbox0=\hbox{\MakeUppercase{\'a\'y\'av}} \showbox0
\setbox0=\hbox{V} \showbox0
\setbox0=\hbox{\MakeUppercase{v}} \showbox0
\stop
So somewhere you must have a definition that is inserting extra tokens
that are breaking the kerns.
David