Hi Akiel,
Do you have continuous stirring/agitation of the tanks during the process?
If not then you'll almost certainly find some settling occurring, and this can create a gradient from top to bottom of the tank for pH, Brix etc.
If you don't have any stirring mechanism within the tank(s), you can gently pump the product round on a loop out of the bottom and back into the top and it will help reduce this effect, but you'll potentially introduce a lot of air into the material and depending on what you're processing and what it's used for this can create other issues (e.g. significant increase in the rate at which browning occurs).
How sure are you that you're achieving a uniform blend when you're acidifying the products?
With pulpier materials like purees it can be more challenging to ensure that the acidifying agent is really evenly distributed throughout the batch. If you've got a tank that'll let you sample from multiple points, or a long "dipper" you can use to sample at multiple depths, then this could also be worth further investigation just to rule it out.
Lastly, if you're pureeing the material yourself as part of the same process, it could be possible that some of the fibrous structure of the fruit/veg is still being broken down in the tank, and this will release further materials into the liquid phase with a consequential effect potentially both on overall acid content and buffering capacity, and thus the pH.