I started having cloudy urine shortly after my last relapse 16 years ago. As with people here, the occurrences happened in conjunction with flare-ups.
My doctor asked me to bring in a sample of the cloudy urine. When I did, he measured the pH and found it to be 8.5. The normal pH range for urine is 4.6 to 8.0; for most people, it's usually in the range of 5.5 to 6.5, with the lower numbers in the morning, and higher numbers in the evening. Lower numbers mean more acidic urine, while higher numbers mean more alkaline urine; a value of 7 is neutral. My blood pH was measured; it was normal.
The most likely cause of cloudy, alkaline urine that occurs during a flare-up is precipitation of phosphates and carbonate salts into crystals. In the presence of a UTI, this can be caused by a urea-splitting organism. Otherwise, the cause is not obvious. But considering that these episodes often accompany flare-ups for us, in these cases it could be a sign of a low-grade infection, which would then be resolved when the flare-up ends.
You can see how alkaline your urine is either by using pH strips, or by dissolving a few drops of vinegar in it. If the vinegar clears up the urine, it was alkaline.
So if your urine is cloudy during a flare-up because it's alkaline, and it returns to clear when the flare-up is over, then it's probably nothing to worry about. However, if the cloudy urine is due to a UTI, the UTI needs to be treated. And if your urine is cloudy all the time, you should see your doctor.