I've seen more posts about this problem and I think I have found the nick of it.
Whenever I change from a computer to another the addons that doesn´t have a true update since the 3.X version but only a compatibility update, doesn't remember of it so I asume that:
1- the data is kept in the registry and it doesn't get saved;
2- there is no real change to the extension so it isn't saved.
I must say that this problem was also with the 3.0 version so it isn't 4.0 especific, but only related with the compatibility updates in either big version change.
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What are you using? Nightly Tester Tools, Add-on Compatibility Reporter, or just plain xpi surgery?
Well I don't used any of that I just compared this with what happened me before (in 3.0 change, what are the news about big version changes every three months?).
I have some addons that are compatible with the new version before big version change and some that have been updated after the version change, those are working OK.
Then I have a bunch of not compatible addons that are disabled. When I connect to the inet some of them get compatibility-updated so they are abled to work with FF4.0.1 after a restart. Then I change to other computer where I have to apply a proxy change to get connected. Normally "quick proxy"-addon will come up and do the change automatically but, as it hasn't been updated but solely autorized to work with FF4.0.1 and there is no network to do the autorization again, all the addons that are in the same compatibility update state don't work. Then I have to do the network change, manually search for updates and restart again FF so it comes up normally.
So to me the problem is that the compatibility updates doesn't reach to the Data directory where the user data should go.
I'm dissecting an extension now(quick proxy). The install.rdf don't show the update(nor before nor after being "updated") it says:
<em:targetApplication>
<Description>
<em:id>{ec8030f7-c20a-464f-9b0e-13a3a9e97384}</em:id>
<em:minVersion>1.0</em:minVersion>
<em:maxVersion>3.5.*</em:maxVersion>
</Description>
</em:targetApplication>
I don't know where the running program data is being temporarily stored so I don't know where firefox says that the extension can be used. But if I keep using PAFF in this computer I will not have any problem and if I change of computer I will have to do the update thing again.
Sorry about the english I'm not used to it.
PD: that led me to a cut&tape solution if nothing more comes up: I could rewrite the install.rdf of the addons I know working.
This is fixed in 5.0. Please refer to this bug report for any further information: https://portableapps.com/node/27310
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