Linking adjacent waterbodies and a bug

For a new lake, I'm helping someone construct the bathymetry file. The lake is set up in the shape of a "H", with two long, narrow sections linked in the middle by a small branch. It appears as if the program recognizes the link, but the W2Control program can't display this correctly in the bathymetry visualizer. The two vertical branches just line up on top of each other, with the linking branch only connecting to the branch within the same waterbody as it. This was also tried with one waterbody, which didn't rectify the situation. In addition, when using the W2Control program with a number of waterbodies is greater than 1, the SLHTC card only allows the options TERM and EQT. However, the only options the w2 code is looking for are TERM and ET, thus EQT is not recognized and unselectable through the program.