Nah, it is just that CuteFTP supports multi-threaded transfers, while FileZilla does not. That's why CuteFTP transfers a single file faster than FileZilla does - just upload more files with FileZilla at once.
But I do agree with you - the speeds are slow, EVEN taking into consideration the fact that the server is in NL. For a 1gbps symmetrical dedicated line, it should be performing far better, even with multiple users on the server. The upload is more like 200mbps, not 1gbps. Even with hosts within Europe or even the NL, it is not giving more than 200mbps, which leads me to believe that even though the trunk may be 1gbps, it may be split between 4-5 servers (not NaHoW's fault, this is the datacenter/host providers fault - but NaHoW should find out and state it in his post).