Here are explanations of simplified versions of the two statements
I do not understand what she is saying
This is present continuous, which generally refers to something that's happening right now. In this case, it means that you don't understand what she is saying right now
I do not understand what she says
This is present simple. It can be used in various ways: in this case, I would take it to refer to something that is always true. Whenever she speaks, you don't understand what she says.
Looking at your original sentences, the construction not always I is not grammatical. When you negate something, you put the word not after an auxiliary verb
I must do my homework
I must not do my homework
If there isn't an auxiliary verb, you add do:
I know
I do not know
So, to make your sentences grammatical, you would say
I do not always understand what she is saying
I do not always understand what she says
These sentences are the same as my simplified examples above, but with the word always added.
In the second sentence, adding always is grammatical and natural: whenever you listen to her, sometimes you understand and sometimes you don't.
For the first sentence, you will hear people saying this, but it would not be correct in formal written English, because always clashes with the right now meaning of the present continuous.