Dot works great most of the time. Sometimes, however, the edges between tables all seem to combine to be equivalent to the first one defined. That is, if you swap these two lines:

TABLE2:PORT1:sw -> TABLE1:PORT1:se; TABLE2:PORT2:sw -> TABLE1:PORT2:se;

you'll get different results.
Input:

digraph relationshipsGraph {
  graph [
    rankdir="RL"
  ];
  TABLE1 [
    label=<
    <TABLE BORDER="0" CELLBORDER="1" CELLSPACING="0">
      <TR><TD ALIGN="CENTER">TABLE1</TD></TR>
      <TR><TD PORT="PORT1">PORT1</TD></TR>
      <TR><TD PORT="PORT2">PORT2</TD></TR>
    </TABLE>>
  ];
  TABLE2 [
    label=<
    <TABLE BORDER="0" CELLBORDER="1" CELLSPACING="0">
      <TR><TD ALIGN="CENTER">TABLE2</TD></TR>
      <TR><TD PORT="PORT1">PORT1</TD></TR>
      <TR><TD PORT="PORT2">PORT2</TD></TR>
    </TABLE>>
  ];
  TABLE2:PORT1:sw -> TABLE1:PORT1:se;
  TABLE2:PORT2:sw -> TABLE1:PORT2:se;
}