You do realise that you can expand each file type group, Audio, Image, Video, Data, etc., in the Auto Import configuration for each folder being imported, correct? You can select exactly which file types are imported for each folder, rather than the whole group. I'm not sure from what you have written. For example, just select "Disk Image Files (iso,img,nrg,mdx)" under the Data group.
As to your earlier problem, search the forum for "Removed Database", particularly posts by Glynor and myself. You will understand some of what was going on.
It is a bit of a querk that MP4 appears under both the Audio and Video groups. So if you select Video, MP4 in Audio is automatically selected, but only MP4. If you then untick the Audio Group, you turn off MP4 in the Video group.
Much of you trouble would have been avoided if you did all your organising inside MC, instead of directly with the file using Windows Explorer.
Glad you got it fixed.