In order to show the subtitles for the appropriate amount of time, the playback lengths of the input files must be the first step. In the wav->aifr conversion window, set the WAV source directory on the left where you saved all of your wavs with the right properties. Then, set the destination directory for the aifr files. The log window at the bottom of the window will tell how many wavs are in each directory as you navigate.

After setting the directories, the press the Get Lengths button. This will save a file called LENGTHS.LOG into the aifr destination directory.