What exactly do you mean by they turn in to normal jobs?
Can you post some screenshots, if possible?
Do you mean SubFolder appears in Monitoring domain as a regular Dummy job?
If this is the case, it is likely SubFolder "Adjust Condition" has recently been selected. With this selected and CTM system parameter "Adjust as Dummy" enabled, SubFolder that is not scheduled for the day will be ordered as a Dummy job.
Correction: Check box "Adjust condition" is likely selected at parent of the SubFolder in question, not in the SubFolder itself.