We cannot know the "why" behind the decision. It could be any of the reasons given above or it could be he has had some balance issues with you in the past or anything. I tended to not use third party stuff in my games.
The first thing you must realize, and I am sure you do, is that if he wants it this way, thats how it is. Thats the GM thing.
The second thing is you must make a guess as to whether or not you have gotten "his final answer" and now the subject is closed or if this is still an ongoing iscussion as to how to get your character closest to what you want.
I would also have approached him with a published feat first. If that failed, i would then approach him with other alternatives, but before i discussed multiclassing, i would have looked for class tweaking as discussed in PHB and DMG. One of the common examples they use is altering class skill lists.
So my second approach would not be toask for multiclassing, but to ask "can i trade off these two class skills for the two that fit my character better?" I would then take that discussion along the lines of what trade offs he would want to tweak the class to fit concept.
I would personally view multiclassing rogue orsuch as a last resort, as it brings in way too much other baggage that can be avoided with a simple tweak to class skills.
As a GM, i allow tweaking of classes routinely. I did it for three classes in my last DND game. I also have begun as standard practice giving every character a free "talented" feat (make one cross class skill a class skill OR gain +1 with one class skill) at first level.
WHy?
Because i have found it common for character concepts to fit the class archtypes "almost perfectly" and that a little thing like one "class skill of choice" helps many people fit the class to the character concept better. They enjoy it more and its a whole lot less cumbersome and focused than telling them to multiclass for one level.
But, thats just me and i ain't your GM.