Dear tzouras,
You did not state in your previous posts that the problem was with all online programs.
Your BitTorrent client is not the cause of the problem. When you first connect to peers and seeders, your speeds are at zero. Soon, you establish connections, and your speeds (down + up) begin to rise.
What might be happening, is for some reason your internet connection if fluctuating madly, or is being disconnected for a short period of time. When this happens, your connections to your download peers and seeders are lost, and you once again have to wait a minute or two to restablish the connections.
The reasons for your internet to be course a few. For one, it may be your ISP's problem, it may be a problem with your computer, or a problem with your network (such as modem or router). Either way, your internet fluctuations are not, or should not be caused by your BitTorrent client. Of course, your downloads will slow down your internet speed while active, but they themselves would not be at zero, and at the same time using up all of your bandwidth.
That said, I might as well give an example. You may have the same, or a similar problem to mine old one. For some bizarre reason, one light-switch in my basement, caused split second of power shortage in one of the rooms, which contained the modem and the router. When the switch was flicked, my modem would reset itself and I would have to wait a minute before the internet was once again available.
Again, your problem might be something completely different, and I cannot pinpoint the exactly problem with your internet connection. Although what I can tell you, is that if your torrent speeds reach zero, along with your browser and such, then it's not a problem with your client. The problem is your internet connection which seems to flux, and your torrents temporarily lose connections to the seeders/peers.
Hope this helps,
-AInTeL