You have to find out what is different in the environment between the two scenarios.
If you run via cron, one could suspect that you run this under different accounts. If so, try to see if that can influence your result.
Be sure to use the same autoexec, config, SAS command shell script.
Try to echo as much information as possible into the SAS log, such as PROC OPTIONS, macro variables. If you are using macro processing turn on debugging options.
Are there any environment variables concerning SAS/ACCESS or Oracle behaviouor, check their values.
Since this kind of problems is hard to debug, it might be a good idea to get a ticket from SAS support.
/Linus
Data never sleeps