Thanks for the info. That makes your situation a bit clearer.
However, I've not see where the .ftm file and media folder have become separated like that.
I would proceed with caution. What would happen if you:
1) Created a new .ftm file with one person in it in the D Dropbox folder.
2) Add a media item to that person.
Does that create a media folder as a companion in the D dropbox folder?
If it does, you might consider leaving your current setup alone, just in case - and:
1) Make a copy of your .ftm file with a slightly different name with Windows Explorer and copy it to your Dropbox folder
2) Make a copy of your Media folder with that same name in the format "name Media" with Windows Eplorer and place it in the D Dropbox folder.
Now open this new file in the Dropbox folder and open some media item to see if opens a media item. Add a media item to it and see if it adds it to the Media folder in the Dropbox.
I go through this same exercise with each version of FTM where I change the year in my file name (ie from 2012 to 2013 in a new folder). That way I always know which FTM program last used that file. I have FTM2011, FTM2010 etc folders with files and media folders in them for each FTM version.
I don't believe the Options > default directory has anything to do with your problem, but could be wrong.