The most recent problems have been with Moodle 2.6 and hopefully what I found can be of use.
a) Ignore all advice about fiddling with timestamps, time functions etc in the admin/cron.php file, it's fine.
b) In lib/cronlib.php there is a section where it runs stats gathering for 'all other' plugins (about line 440). Unfortunately there are some filter and repository plugins that appear not to have been written correctly and so when the cron reaches this stage it throws an error and dies. As yet I have not had the time to determine which specific filter(s) or repository is causing the problem, so as a stop gap I comment out those functions and stop them running. I think there needs to be some stricter testing imposed on non-standard filters / repositories to prevent this at source.
c) When processing the logs and getting them in the desired format for insertion into the stats tables, the data is understandably stored in temp tables first. Unfortunately it appears that the field sizes of the temp tables do not match those of the log table and so data can not be inserted and the process stops. This has been a particular issue with the action field for example with the value "moodle_user_get_course_participants_by_id". This may have been fixed in 2.7 but if not it's worth having a look at.
Using Moodle is a huge part of our curriculum delivery and the more stats the merrier as far as my senior managers are concerned, so I'm looking forward to looking at the additions for 2.7