I am experiencing the same problem. Whenever Download Station is active other internet connected applications suffer badly. I am aware of the possibility of changing the settings for bandwidth limitation but this does not seem to help.
The following examples have these starting prerequisities: All torrents in DS are finished downloading and the maximum upload limit is set to 60 KB/s (this is most often maxed out but it is well within what my internet connection is capable of).
A friend calls me on skype. I answer the call and soon realise that the connection is totally garbled and Skype itself reports that there is a bad connection between me and my friend. I go into DS and lower the upload limit from 60 KB/s to 5 KB/s and watch the actual upload speed go down to this number. Unfortunately this doesn't make any difference for Skype call quality. I go into DS again and pause all torrents whereafter Skype call quality immediately becomes excellent.
I fire up Left 4 Dead (or any other ping-dependent game) for some FPS-gaming. I join an internet game and quickly finds the ping to be unbearable, jumping constantly and most of the time being between 500 and 1000 ms. I go into DS and lower the upload limit from 60 KB/s to 5 KB/s and watch the actual upload speed go down to this number. However, this does nothing to improve my ping in Left 4 Dead. I go into DS again and pause all torrents and upon returning to the game I discover that my ping is now where it should be, roughly between 20 and 50 ms.
It very much seems that Download Station hijacks the internet connection totally no matter what bandwidth limits are set. I am on DSM 3.1 for the moment but during the use of DSM 2.x I used transmission for a while and I never experienced any of these problems. Maybe this is something which has been corrected in DSM 3.2 which I am upgrading to soon.
Well, let's see if someone else also have had the same experience and possibly solved the problem.
Nice forum by the way. Lots of good info here! =)
Model: DS1010 F/W: DSM 4.0-2228 HDD: 5 x WD RE-4 2TB WD2003FYYS (RAID5)