What you describe sounds VERY much like a networking issue of some kind, as totallymaxed suggested - that performance is nowhere near normal even for 100Mb.
1. auto speed or duplexing issue either on the NICs or switch ports - although this is usually less of an issue now with Gb LANs. Is your switch manageable - meaning you can connect to it and configure it, or is it black-box?
2. try getting a cross-over cable (usually red) and connect the MD directly to the core, thus eliminating the switch and normal cables, to see if that makes any difference. this is a good first test to try.
3. packet loss somewhere between core and MD, due to cables, connections, switch or NICs. if over a few percent, this will cause TCP to have to retransmit and backoff - this will cause a dramatic reduction in performance. can be caused easily by either of the 2 points above.
4. incompatibility between the NICs and the switch hardware - test 2 will also highlight this immediately.
5. some issue with the NICs themselves, or more likely the drivers - check the versions, and the model of Realtek you are using with the ubunutu hardware wiki. EDIT2: another thought, I read somewhere in the last couple of days that the Realtek 8169(?) Gb NIC was small and cheap, but that person had a very hard time getting Gb speeds out of it with Ubuntu... more like 100Mb, that being said, you don't even seem to be getting 100Mb speeds!
6. bit difficult with a diskless MD, but an ideal troubleshooting test is to navigate to a remote share on the core from the MD, or vice versa, and copy a large (50MB+) file over and time it. work out the rate from this. the linux dudes will have to help you with where to copy it too - perhaps a ramdisk?
7.failing the above test, you could use a PC (with disk, say Windows) navigate to the core and test, then the MD and test again - this doesn't give you end to end, but it could be indicative...
8. use the performance monitoring tool on the desktop, and add the bytes in/out per second counters and watch the traffic profile whilst copying a file, and booting from LAN. Whilst copying the file, you should see it ramp up fairly quickly then stay reasonably stable (assuming no other traffic on the network) until the end of the file. not sure what to expect for the MD boot as this uses TFTP which is a UDP protocol and so doesn't use the same congestion control mechanisms - at a guess, it would ramp up much quicker, but then be fairly erratic - guesstimate an average throughput
oh, finally, I forgot to say, auto duplexing and speed issues in your configuration will often only manifest a throughput performance issue in one direction, or heavily tilted in one direction. So when you perform the file copies, etc, test both directions, but especially from core to MD, obviously!
EDIT: one more thing, there will be linux tools for capturing information like TCP resets, retransmits, errors, etc, which would point you to the problem as all of these dramatically impact network performance, but I do not know linux at all, so again the linux dudes may be able to give you pointers there.