This is indeed fixed in the current svn, install using:
$ sudo apt-get install gnome-common python-gtk2-dev subversion libgconf2-dev
checkinstall
$ svn co http://svn.infinicode.org/computertemp/trunk/computertemp
$ cd computertemp/
$ sh autogen.sh --prefix /usr
$ make
$ sudo checkinstall -D --pkgname "computertemp" --pkgversion "0.9.6.1.svn`date
+%Y%m%d`" --default
** Changed in: computertemp (Ubuntu)
Status: Confirmed => Fix Committed
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computertemp has an opaque background and it should be transparent
https://bugs.launchpad.net/bugs/362155
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