OK, this looks to be an application setup problem rather than anything to do with the network or NAS.
As I understand it both those programs download data from usenet to your computer. This process can take time and is designed to work best if the storage directory is on the computer that is doing the downloading. The fact that you are using the NAS as the storage directory and neither of these programs have been optimised, as far as I know, for network usage there might be your problem.
If you are into programming you can download the source for CouchPotato from GitHub and see if you can improve the networking transfer speeds. Other than that it looks as if the fastest way is to download to your computer and then either do the manual transfer or setup the NAS to backup the directory you use for storage at fixed times. I know this is not what you want but sometimes we have to do the best we can when trying to get programs and storage to work together, sorry.