There is no such thing as a "custom AES implementation". If any detail of it is changed, it is no longer AES. AES is the standard that describes to precise detail how encryption using AES is done.
NIST gives certification to those who implement AES correctly and safely. You may have implemented it so it gives the right answers, but the way you did it could lead to problems. For example, if you multiply numbers in such a way that 250 is quicker than 350, an attacker could notice that and make use of it. This is what NIST is certifying for.
Now there are different "modes" of operation. These modes are not part of AES, but rather how you put blocks of AES encryption together. See this wikipedia page