Don't they use the sharedband service to provide their bonding?
You could go through the guide here
to see if that helps to pinpoint the problem.
I would test each line individually if possible when the slow down happens to eliminate or confirm the bonding service as the problem.
The sharedband service tests the line speed at intervals to set how to spread the load across the lines. Maybe turning up the frequency of the test might help to cope with some slowdown.
As a last resort and if it is provided using licensed Sharedband you could be cheeky and phone the Sharedband tech line for advice.
I had a long chat with their presales technical line who seemed really clued up. If I remember correctly having just one erratic/faulty line could cripple the overall speed.