This is something you should probably discuss with your Dr. or a gastroenterologist who can help determine the underlying cause.
Aside from diverticulosis/diverticulitis, I am not aware of a GI disorder that is sensitive to berries and their seeds.
I have heard before that some people are sensitive to certain pesticides or herbicides so if you are not using organic produce then I'd for sure switch to it. You may also have a specific food intolerance or allergy that is triggered by compounds in the berries and nuts.
I'm not sure I'd call it a "buffer", but when you add banana and avocado, this helps bind the ingredients in a Blast to make it more smooth.
When thinking of replacements, a good guide is often color -these are the phytochemicals that make up the fruit/veggie. So for red/purple berries try some beets, dried goji berries, tomato or watermelon, purple grapes (seedless), plums, or black beans. Blueberries are great if you can eat those without issues.
For protein and healthy fats that are found in nuts - maybe some hemp, chia or flax seeds will work!