Y'all should check your cables. The little SOHO routers whup right along, easily keeping up with Fast Ethernet. 
If the cables are hand made (by you or some person you know that's not a cabling professional), then chances are (that'd be about an 80% chance, according to industry specs) that your cables are bad. Even store-bought pre-made cable can go bad with the right kind of abuse. Just because you get some data through, don't assume your cables are allowing max performance.
After the cables, it could be related to your hard drive speeds, the OS, amount of RAM, other background programs, cheap NIC, crummy / out-of-date / wrong drivers, slow chipset, slow application, etc. There are A LOT of things that can affect your throughput, but the SOHO router should be WAAAAAAAAAAAY down on the list, somewhere just above the SOHO switch. If one of the systems is a laptop, then you can automatically almost double the time; laptops are very slow compared to a similarly equipped desktop (the price you pay for portability and long (snicker) battery life).
BTW: being in separate workgroups would have no effect on the performance (at least after the session is established, if at all).
JM.02
Scott