Well... there's a couple of ways around that (if you want technobabble from a molecular biologist ^^ I'm just giving a basic rundown from my view - I can get really technical if anyone wants a rationalization of the molecular biology of metapower expression)
Since I've never read the IST books, and can only go from what I've read here...
The Cavillo test would be for the transcription factor that binds to all the other metagenes. All genes have promotors of various types where the enzymes that read the DNA bind to initially, then goes on to read the gene. The transcription factor is what connects those enzymes to a given promotor - since there are different transcription factors, it allows different genes to be expressed in given cells (genes only in the brain vs those expressed in the liver).
There are several ways to track down which genes the Cavillo factor would bind to, to figure out which metagenes are expressed, and from that try to figure out what their powers are. Although determining what their powers are from gene expression could be really difficult (there's various levels of interaction from multiple areas that can change what that gene does or express). While the IST world would be more advanced in genetic engineering, there'd still be enough (IMO) cloudiness possible for people to not be testable for specific powers. It'd get more complicated (and fun!) if one of the things that the Cavillo factor activated were more transcription factors, leading to more pathways to chase down.
As far as having powers undetectable via the test...
Mutation in the gene - the metagene activation factor isn't going to have selective pressure on it to keep it from spontaneously mutating. Perhaps they only THINK they're getting 100% of metahumans. Alternatively - that person had a mutation in a different transcription factor, one that now allows that transcription factor to bind and activate metagenes. This could be a general activation, or it could be selective to only one or two metagenes.
Pseudogenes, siRNA, microRNA, post-translational processing...
The test for metahuman genes can be just as effective/ineffective as you want/need for the world to have.
RMH
Since I've never read the IST books, and can only go from what I've read here...
The Cavillo test would be for the transcription factor that binds to all the other metagenes. All genes have promotors of various types where the enzymes that read the DNA bind to initially, then goes on to read the gene. The transcription factor is what connects those enzymes to a given promotor - since there are different transcription factors, it allows different genes to be expressed in given cells (genes only in the brain vs those expressed in the liver).
There are several ways to track down which genes the Cavillo factor would bind to, to figure out which metagenes are expressed, and from that try to figure out what their powers are. Although determining what their powers are from gene expression could be really difficult (there's various levels of interaction from multiple areas that can change what that gene does or express). While the IST world would be more advanced in genetic engineering, there'd still be enough (IMO) cloudiness possible for people to not be testable for specific powers. It'd get more complicated (and fun!) if one of the things that the Cavillo factor activated were more transcription factors, leading to more pathways to chase down.
As far as having powers undetectable via the test...
Mutation in the gene - the metagene activation factor isn't going to have selective pressure on it to keep it from spontaneously mutating. Perhaps they only THINK they're getting 100% of metahumans. Alternatively - that person had a mutation in a different transcription factor, one that now allows that transcription factor to bind and activate metagenes. This could be a general activation, or it could be selective to only one or two metagenes.
Pseudogenes, siRNA, microRNA, post-translational processing...
The test for metahuman genes can be just as effective/ineffective as you want/need for the world to have.
RMH