Symptom:
when creating a new custom system data variable, the variable is added to the job definition however when creating new jobs the new custom system data variable is not available requiring you to manually recreate each time.  This is different behavior from the web client

Conditions:
using java client

steps to recreate
1) in job definition click variables
2) click system variables
3) click system date variable
4) click date format
5) pick the order /  formate you want for the variable and click add custom format and click ok
Results
newly create variable is added to job, if you go back to the system variables the newly created format is not there - do the same in the web client and the variable gets saved.