Allright, there seems to be a solution:
Just put a call to fix_permissions to /system/etc/install_recovery.sh:
Code:
#!/system/bin/sh
sh /system/bin/fix_permissions -l 2>&1 > /data/fix_permissions.log
I had several crashes when trying stuff / installing apps, etc., which needed a reset, but I did not face any more force closed popups or lost settings!
Credits go to
S3raph.