1) If you believe there is something wrong with your system, but do not include your installation method with version ... well, please do from now on, LOL.

2) "some calls"? How about you describe this situation a bit more clearly: Which log file? Or which table name? How was the missing call generated?
3) In response to the above, when you say "not one, lots of them!" I'm still going to ask for ONE missing call, and how it was generated. Tracing one call, and why one call appears in specific logs, or doesn't appear in others, is pretty easy.
4) Guessing about "some calls": Because they do not belong in the log you're looking in. Inbound calls land in the inbound logs, transfers are in the closers logs, oubound calls that are autogenerated appears in others ... note that "log files" are merely for troubleshooting whereas log tables are for reports. If there is no report that needs the data, there's no need for a log table. Perhaps you should begin with a report that shows the calls you're talking about, and then add "&DB=1" to the URL and find out what queries may be used to generate that report (which would give you the table names).