Hi, I'm new to Mediacoder and to the forum so firstly, thanks for an excellent product.
I'm using Mediacoder AE and, like others in the forum, I have found that the Preserve Folders option does not work when folders are added recursively. It does seem to work if individual folders are added one by one, but that is a pain if you have a lot of nested folders.
I tried dragging and dropping folders from Explorer into the Mediacoder window as others suggested, but this does not recurse down the nested folders; it just adds the files in the top-level folder dropped.
So here's a possible workaround.
Use Windows Explorer "Search" function to find all of the files you want to transcode, starting in the top level folder. For example, search for "Files and Folders" with a pattern of "*.flac", in "D:\My Music". and make sure that Advanced Options has "Search Subfolders" ticked. If you have multiple patterns, separate them with commas, e.g. "*.flac, *.mp3"
This will find all matching files in the top level and all sub-folders.
Then from the Search Results window, select all of the found files (CTRL-A) and drag and drop them into the Mediacoder window, with the Preserve Folders option set.
This worked for me, I hope it helps someone else too.
Thanks again for an excellent product