Hello,
there errors are not caused by incompatible names, but simply by too many uploads too quickly. You may want to set the number of files being copied in parallel to 1. This can be done on the Files tab sheet in the profile. Also make sure that only one profile/job runs at the same time.
If you do believe that some folders or file names are incompatible, please give me some examples. Also, you should see different errors (not only request_throttled).
Maybe there are other errors but they are not logged. To get more detailed logs, you can turn on "Internet Protocol Logging" on the Logs tab sheet of the Program Settings dialog. This will also give you IPLOG files. The paths to these files are listed in the main log file.