I know what you mean. Usually when I get a feeling about someone and I just have a sense they are not on the up and up or they are manipulative or they are passive aggressive or they are narcissistic I am not able to pinpoint it at first. After being around them for awhile I will see it more clearly though and it usually takes awhile before they finally show their true colors to everyone else.
Personally, if I were in your shoes I think I might let my son know I have reservations about her, I am only telling him this because I want him to be happy and I will support him in whatever decision he makes. Reason being is in the past I have ended up looking like an ass in the beginning for writing someone off without them having shown their true colors to everyone else. She will eventually show her true colors and you can be there for your son when she does. Sit back and observe. Your son will need to see for himself how she is. Encourage him to take his time and really get to see how she is in group settings and with family. Be willing to support him because he is going to do what he wants anyways and you don't want him not coming to you with problems for fear you will tell him "I told you so".
Just a side note: Some of my closest friends and some of my worst enemies have been the ones I initially hated on gut instinct. So who knows, maybe you two will be thick as thieves eventually.