Also, having gone through this "waiting" process. You may have to delete and up load again, but if you received that all was ok after the upload, there are other avenues to pursue.
For example, I have a Mac, and tested through FT, after many attempts to upload raw data I contacted FT. Finally had a response from FT saying that some Mac computers carry a built in "feature" (?) that protects and puts the unopened zip file, the "good file" in the trash and then places other files in your download folder, which you can see but they will not upload properly to Gedmatch.com.
Once new files were downloaded, removed from trash, and re-uploaded to Gedmatch.com, all went through in a matter of hours.