Mr Faber,
I also use traffic shaping, and also have this kind of "problem" (quotation marks because I don't really care). The thing is, it's not a problem, it's just your side of the HTB queue. Delays and spikes are in a close relation to queue length. Say you have a queue length of 100 - i.e. the shaper will queue 100 packets for you. aMule will fill those 100 packets in no time - therefore a spike in the upload speed, and won't be able to send any more data (will be dropped, if it does) until a certain percentage of the packets get dequeued. This will show in your graph as 0.0.
On the other side of the shaper there's a smooth flow of traffic - you can see it, if you put another machine between the one with the shaper and the internet connection, as a gateway. You'll see a constant steady upload speed.
You may be able to reduce those "incative" times and lower your spikes by reducing queue length on your HTB shaper. But keep in mind that shorter queues also affect badly the shaper performance itself, i.e. it won't be able to shape so nicely.