To replay a Clip, you have to stop it and reposition it, then start it. I don't think you can close and reopen a given Clip. But attempts to do that should have generated a LineUnavailable exception, and you say you got no exceptions.
To troubleshoot, I'd first verify that it is possible to play the .wav files prior to placing them in the hash table. Sometimes an unexpected format (e.g., 24-bit or 32-bit encoding, or big-endian rather than little-endian) can lead to .wav files not playing.
If you are trying to concatenate a series of clips or audio data into a single clip, that could also be problematic. I think that AudioInputStream expects a single set of "header" data from the .wav file, but the SequenceInputStream could in effect be sending multiple "headers", one for each source file. I've never seen concatenation attempted like that before.
You might need to make your own data storage for the raw audio for each phoneme, and then build your combined phonemes from that rather than directly from .wav files. Instead of loading to Clips, load the raw PCM from the AudioInputStream into byte arrays. To output the raw audio bytes, you can use a SourceDataLine.