Thank you for the post.
I am unable to replicate this. While I did not have access to Google Drive for testing, I was able to successfully upload a file from a custom icon subfolder inside a custom icon subfolder in a shared folder that also had a custom icon.
Folders or subfolders with custom icons do not seem to make a difference when uploading a file to FileMaker Server. I tested on Mac OS X 10.8.3 with FileMaker Server 12 Advanced and uploaded from a custom icon two subfolders down located within a shared folder for a Windows 7 virtual environment.
Does this only happen with Google Drive folders?