#3: please see:
http://docs.moodle.org/24/en/Automatic_updates_deployment#Can_not_download_the_package
for possible resolution.
#2 few courses cannot be backed up
Was debug on when attempting backup of those courses?
This is a tough one ... due to number of possibles, however, do those courses have something in common? ie, a block or activity NOT used in courses that can be backed up. There could also be something in a label (which, BTW, may have caused issues with previous versions of Moodle as well, but you've just discovered the backups issue cause you finally have arrived at the destination via the 'moodle march').
Things to check ... after a failed backup of a course, use whatever you have to browse the moodledata folder /temp/backup/ Successful backups record a 0 byte .log file. Un-successful backups create .log files that are larger than 0 bytes. The .log files are text so you can open to inspect what they say.
Backups will create a long folder name in moodledata/temp/backup/. Inspect one of those folders. This is where Moodle attempts to build the zip (.mbz). Sometimes one can find strange things in there that might have been issues before but just now noticed.
Also check apache error logs ... sometimes one can get a clue there as well.
'spirit of sharing', Ken