When creating a Custom Timesheet that has either a JQL or extra fields, those settings get lost when timesheet is saved.
In the screenshots attached, I create a new custom timesheet "Test", give it a JQL and an extra field to show on the report. The first time after Applying the Save As timesheet, it works, but when added to main menu and run from there, or when re-edited in custom timesheets, these settings are gone.
Step 1 - starting to define:
Step 2 - Define JQL:
Step 3 - Define custom field to include in report:
Step 4 - Save it as "Test":
Step 5 - Apply the report from the custom timesheet editor (custom field is included):
Step 6 - Add to the main menu:
Step 7 - Run from main menu (custom field is gone):
Step 8 - Re-enter custom timesheet edit (JQL is gone, custom field exists although not honored by repor):