I've throttled my uploads, and the bandwidth throttle works here, so don't understand your situation.

The limewire.props files doesn't list speeds in KB/s (.25 = 25 % of bandwidth set, IIRC, 1 = 100%).

I can see peaks in the tools->bandwidth->uploads graph over the limit I set, but the averages work correctly. Are you seeing higher averages in that graph than you've allowed in the upload options?