Wavetable cents/tone errors

I play midi on my computer through the "Wavestream Music
Synthesizer," a driver that uses a software wavetable. Some of the
sounds are pretty good, a lot better than the awful onboard sound
that came with my Hewlett Packard Pavilion 6355. I'm creating a
program now that will eventually play sounds with alternate tunings.
At this point it will play sounds in 5 cent increments. I've found
that many of the pitches not equal to modern equal temperament notes
produce a horrible tone quality. Move 5 cents up or down to a
standard pitch and it sounds good.

Is this just poor wavetable software, or is this a typical problem?
Thanks.