A couple of questions and some things to check...
(1) What release and platform are you running on? Please update your signature with this information as it could make a difference.
(2) Are the "jobs" that you don't get logs for running in deferred mode? If they are, check the SCHEDULER to make sure it has not crashed.
(3) Are these "jobs" process flows, data flows, Data Migrator stored procedures, or a combination of the three? If you use a lot of stored procecures and don't have -SET &ECHO=ALL in the top of it, you should still get a log but you won't see much.
(4) How large is your log file? This probably isn't your issue if you're getting logs for some things but this is always good to check. Depending on the release you are on, there is a 2GB limit.
(5) Have you looked in your DFM_DIR directory? When jobs are run in deferred mode, their info is first written to "temp" files in the DFM_DIR directory, then when the job is done, the info is written into the actual log file. If you don't have anything currently running but there are files in the DFM_DIR directory, that could be your missing logs. The only way I know to deal with this is to rebuild the log. If you don't want to do that, or want to know if there is another way, open a case with IBI.
Data Migrator 5.3, 7.1, 7.6
WebFOCUS 7.1, 7.6, 7.7
SQL Server, Oracle, DB2
Windows