It is enough to show that the intersection of two finitely generated semigroups inside a finitely generated commutative semigroup is not necessarily finitely generated, for then you can consider the semigroup algebras.
So let AA be freely generated by y,zcupxn:ngeq1y,zcupxn:ngeq1 subject to the relations yxn=xn+1yxn=xn+1 and zxn=xn+1zxn=xn+1 for all ngeq1ngeq1, and xnxm=xnmxnxm=xnm for all n,mgeq1n,mgeq1 (notice that AA in fact coincides with the given set of generators...). Let A1A1 be the subsemigroup generated by yy and x1x1, and let A2A2 be the subsemigroup generated by zz and x1x1. Then AA, A1A1 and A2A2 are finitely generated and commutative, yet the intersection A1capA2A1capA2 is the subsemigroup of AA generated by xn:ngeq1xn:ngeq1, which is isomorphic to mathbbNmathbbN under the product. This is not finitely generated.
Later: Yemon asks in a comment if one can change this so that the containing algebra is a domain. I think this works: let AA be the algebra generated by y,z,ucupxn:ngeq2y,z,ucupxn:ngeq2 subject to the relations yxn=xn+1yxn=xn+1 and zxn=xn+1+uzxn=xn+1+u for all ngeq2ngeq2, and xnxm=xnmxnxm=xnm for all n,mgeq1n,mgeq1, let A1A1 be generated by yy and x2x2, and let A2 be generated by z, u and x2. (I have to remove x1 for otherwise x1(x1−1)=0)
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