Report 1.
Try to remove the entry in "Configure Your Desktop -> Startup & Shutdown -> Autostart".It should not have an entry there and this entry could explain the second instance.
I now know where the item in Configure Your Desktop -> Startup & Shutdown -> Autostart is coming from.
And I will come back on this tomorrow.....
And here it is..... and toke me a lot of testing today and this is what I did and its result.
(to make the notation shorter Configure Your Desktop -> Startup & Shutdown -> Autostart=desktop_autostart-item and autostart fromqt-update-notifier=notifier_autostart)
I did a new installation on a separate partition with pclinuxos-kde-2013.04.iso (new / and new /home).
This one has qt-update-notifier-1.3.0, desktop_autostart-item
and a marked notifier_autostart after the installation.
Multiple restart of the system did result in a
single instance of qt-update-notifier everytime.
After the update qt-update-notifier-1.4.1 is installed and desktop_autostart-item
and a marked notifier_autostart are still present.
A restart will now result in a
double instance of qt-update-notifier everytime.
This can only be solved by either removing desktop_autostart-item or removing the marking from notifier_autostart.
I can't detect whether the desktop_autostart-item is from the rpm package or the draklive-install script.
One thing is for sure and that is desktop_autostart-item is present after a new installation with pclinuxos-kde-2013.04.iso and every new installation or re-installation will encounter this problem.
Report 2.Previous versions of qt-update-notifier had different function when you clicked "Open Synaptic".
Synaptic opened, reloaded the repository indexes and automatically marked the available updates.
Now you have to manually hit on Reload and then Mark All Upgrades.
I believe this is what atolboo was trying to say...
I remember there was a discussion about this function and some users didn't want it...
this was the automatic reload when opening up Synaptic. This functionality is broken because when you then click on Reload again Synaptic will crash. For this reason this functionality was removed in recent version of qt-update-notifier.
-p.
qt-update-notifier-1.3.0 (from pclinuxos-kde-2013.04.iso) has this automatic behavior (without a Reload in Synaptic)

@pinoc
I did Reload multiple times and Synaptic never crashed (this was also re-tested multiple times) and the update (18 new, 159 upgrades and 4 removed) produces no problems.
That's my observation.