JSGME will only give you a warning when its changing a file thats already been altered by another mod
If you add say a sound mod and its the only sound mod you have added then JSGME will say nothing
Add a second sound mod that overwrites some of the first mod THEN you will get a warning message
Doesnt mean it will be a problem just letting you know so you can check
JSGME v2 may have cured that - not had time to look into it yet