A fix has been located. However, I am hesitant to call this issue
closed. Let me explain:

I found a Tribe 5 x86 user with a working prefs.xml ("rsk" in #ubuntu+1). 
Checking his vs. mine, there was a very important difference:
                <pref name='plugins'>
                        <pref name='loaded' type='pathlist'>
                                <item value='/usr/lib/purple-2/autoaccept.so'/>
                                <item value='/usr/lib/pidgin/notify.so'/>
                                <item value='/usr/lib/purple-2/ssl-nss.so'/>
                                <item value='/usr/lib/pidgin/pidginrc.so'/>
                                <item value='/usr/lib/purple-2/ssl.so'/>
                        </pref>
                </pref>

Versus mine:
                <pref name='plugins'>
                        <pref name='loaded' type='stringlist'>
                                <item value='/usr/lib/pidgin/docklet.so'/>
                                <item value='/usr/lib/pidgin/notify.so'/>
                        </pref>
                </pref>

Note that when I used his, new plugins would appear as loaded whenever I
added some, or would be removed from the list when deselected. With
mine, the list always appeared as above. Changing my type to pathlist
would only make it revert, as would adding any plugins. What I finally
had to do was change it to:

                <pref name='plugins'>
                        <pref name='loaded' type='pathlist'>

                        </pref>
                </pref>

After relaunching Pidgin, I could re-add the two items, and any plugins
would automatically move in/out of the list as expected.

This fix was confirmed *to an extent* by a Fedora Core 7 user, Joseph
Adams. He did NOT have docklet automatically added to his prefs. It is
our suspicion that docklet.so may be the offending lib. Perhaps it was
still being utilized/looked for after the closing of Pidgin, thus the
forceful reversion to the non-working "stringlist" type? But why would
that happen initially at all?

Keep in mind the second time I tested this was on a fresh install with no 
additional packages loaded.
What is this docklet.so? dpkg -S docklet.so returns no results, and with good 
reason: /usr/lib/Pidgin/docklet.so does not exist! There is some discussion on 
developer.pidgin.im about making Pidgin more aware and able to utilize X11's 
docklet. Can anyone provide more information about docklet.so, and any possible 
role it played in this issue?

-- 
Pidgin 2.2.0 Forgets Plugin Selections (Ubuntu Gusty x86 Tribe 5)
https://bugs.launchpad.net/bugs/144122
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Bugs, which is the bug contact for Ubuntu.

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