I am seeing this exact same behaviour (Ubuntu Feisty, 7.04) but in my case 
I have recompiled one package (screen), using the src .deb package, and 
following
all the recommendations to generate a new .deb package and installing this one, 
so that I can receive notifications about *updates* (i.e. new versions or bug 
fixes).

I needed to do this because I wanted screen compiled with certain configure args
that are not used to make the original ubuntu package.

However, apart from building the package with other configure arguments, the 
version
is the same. Nonetheless, update manager tells me that I have 1 update 
available:

screen
a terminal multiplexor with VT100/ANSI terminal emulation
>From version 4.0.3-0.2ubuntu2 to 4.0.3-0.2ubuntu2

The two packages differ in size, however, so maybe update-manager is basing
its decision to notify on this?

Perhaps you can modify update-manager so that we can choose to omit 
notifications
of updates to the *exact same version*?

How to reproduce:

1. Uncomment the deb-src lines in /etc/apt/sources.list

2. Install all dependencies required to *build* <pakage-name>
sudo apt-get build-dep <package-name> (screen)

3. Get and unpack the sources
sudo apt-get source <package-name> (screen)

4. Edit one or more files in the src, apply a patch, etc.
    In my case, I just changed two lines in screen-4.0.3/debian/rules

--- screen-4.0.3/debian/rules.orig      2007-08-01 12:25:55.000000000 -0300
+++ screen-4.0.3/debian/rules   2007-08-01 12:26:04.000000000 -0300
@@ -27,8 +27,8 @@
                    --with-pty-mode=0620 \
                    --with-pty-group=${TTYGROUP} \
                    --enable-rxvt_osc \
-                   --with-sys-screenrc=/etc/screenrc 
-#                  --enable-colors256
+                   --with-sys-screenrc=/etc/screenrc \
+                   --enable-colors256
        touch $@
 
 build: build-stamp

5. Recompile <package-name>
cd into the unpacked sources directory (screen-4.0.3) and run
sudo dpkg-buildpackage -rfakeroot -uc -b

6. Install the recompiled package
sudo dpkg -i <package name>.deb

7. Notice how update-manager stupidly tries to make you install the original
package over your customized package.

8. It's annoying, and if you forget to uncheck your customized packages can lead
to disaster if the packages are critical ...

-- 
Shows pinned packages as available to update
https://bugs.launchpad.net/bugs/52158
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