Is the sequence IPAGRG always going to be Negative, or does it depend on what is around it?
Is IPAGRG a commonly-occurring subset?
When IPAGRG occur together, will they always have the same positivity.   That is, will IPAGRG always be either 000000, 111111 or 222222, or could it be 012201 etc?
I think you somehow need to have a single “answer” for each sequence that you give to BERT, so that it can learn.
(I’m a bit worried that if you give it a label such as 22222111111222222 it will treat that as a single numerical value, which is not what you want).
Could you treat IPAGRG as a single token, and DGQPE as another, and EHPQGI as another, so that BERT could try to learn to predict the value (positive/negative/unknown) of the central sequence in each input of 3 sequences?
From your Masked prediction success, it seems that there must be some common sequences.   If you don’t have any a priori idea of what these might be, you could maybe try an n-gram analysis.
Completely different idea:
Could you use 60 tokens instead of 20, where each token includes information about the amino acid AND the positivity?
So,
token A0 could represent alanine with positive,
token  A1 could represent alanine with negative,
token A2 could represent alanine with unknown.
By the way, it’s not relevant to the BERT implementation, but what do the positive/negative labels actually signify?