Curious experience with Maverick/Natty/home directory

[MR ZenWiz]

I had Natty on my newest laptop (a used HP NW9440) and it was running
more or less smoothly with the "classic" (i.e., Gnome 2) Ubuntu GUI.

I got it a shiny new 500GB disk drive and decided to back up all of my
desktop home directory files on it as a precaution (I have other
backups).  I still run Maverick on the desktop, though I should point
out that I have a fairly customized window environment with a custom
theme and colors and window-widgets, courtesy of metacity and my old,
CentOS 5 base that I moved off of back in October of last year..

I thought it would be a simple rsync -av from the desktop home
directory to the laptop home directory, but some things didn't exactly
work out quite right.  For one thing, the environment was different -
radically different.  The windows all came up with no title bar or
borders, and none of the "standard" windows manipulation commands
worked, including <alt><f4>.  The windows all came up in the top left
corner, regardless of how many were up or if there was room for a new
one elsewhere, and on.  Most of my keyboard shortcuts were gone (!),
and among other things, the Workspace Picker wouldn't let me select
how many workspaces I wanted or how to display them - it only allowed
1.

All the command line commands worked fine, more or less, so I was able
to get around, but this quickly reduced the laptop to a useless
appendix I couldn't work with.

I thought maybe this was just a Natty-Maverick incompatibility, so I
reloaded the laptop with Maverick, installed a few basics and did the
same thing.

Same effect.

Now I'm not usually this thick, and I realized I should have copied
the files over to some other place and moved the relevant ones into my
home directory, but it took me twice to get that and I wound up
reinstalling Maverick again before I did that, at which point all is
well.

I'm just wondering what kind of gross environment muck-up could cause
that kind of havoc - which control/config files in my home directory
could make so much trouble and disable so many things.

TIA.