First of all, take a look at the dat and check how they organized the sets and if you use a correct rompath setting. Keep in mind to follow the supported storing method:
rompath\setname\file 1 ... file n for decompressed sets
rompath\setname.zip(.rar, .7z) for compressed sets.
Second thing with N64 files is: Headers and Byte/Word Order, i.e. one and the same file (datawise) can be stored in a different byte/word ordering which results in a different hash. Different hash -> cmpro's name check won't find a match.
In clrmamepro you have header support (settings->headers (rompath dropdown box)). There are several header definitions there for N64 files for the different byte orderings. You can try to play around with them.
Maybe the nointro datfile even provides an own xml header definition (which should be listed in the header of the datfile and you should get it from somewhere and put it in cmpro's header folder before starting cmpro).....Since I don't know the datfile, I can't tell you.....so check out if one of the standard n64 headers help you....or convert your files in the format which the dat is made from....