Elastic Audio has several different quality settings. If you are doing real-time conversion, things are going to have artifacts. The x-factor setting requires processing but gives a much better result, especially with the "Formant" engaged. The Formant switch helps preserve the upper harmonics which are what affect the amount of artifacts in the conversion. You will hear the real-time conversion which might sound funny but once you have adjusted the region to conform with the tempo change, taking the elastic audio off will ask you to commit or process the waveform. After you process you will hear the better sounding result.
Make sure to duplicate a playlist with audio so you can get back to the original easily.
Also, it makes a difference whether your tracks are set to Samples or Ticks. Consult the documentation under Help>ProTools Reference Guide. PT has great docs right on screen but people seldom use it :)
Make sure and use the "Monophonic" setting when manipulating bass. The "polyphonic, monophonic, rhythmic options are also all important for the various other instruments. Not to totally disagree with Bret but I've found on a recent project that when I did the elastic audio on drums it sounded better when I didn't actually print or commit or process. Maybe I'm wrong but test the theory and decide.
I've run into that. Different program material, different A to D converters and different sample rates can all lead to different artifacts and hence different results. I found elastic audio sounded lots better at 96k. I also found that, much to my surprise, the old WAVES soundshifter plug run audiosuite at 96k could beat it every time.
This probably won't fix your problem but it may help a little. I've found that when you're using elastic audio on guitar tracks, especially bass, or really anything besides drums, it helps to go through, move your warp markers to where you want them, switch to analysis marker view and delete all of the analysis markers. If you remove unnecessary warp and analysis markers, you may notice some of the unwanted artifacts will be gone.