I'll keep a close eye on things for a day or three.
Thanks.
There were a number of permission problems - because I install these things in a way so the webserver-user cannot do serious damage, in case some unknown vulnerability gets used, however for upgrades, the webserver of course MUST be able to do nasty things like deleting/modifying files :-)
Anyway, all files are back to their safe ownership and permission after the upgrade.
/Lennart