I don't know any thing about this stuff but, is the update code that you injected the same code that also checks if an update needs to be applied?..
In other words, the code that *checks* might still not have been over-ridden maybe?.. (Even though the actual update on the cart is now 9.2)..
The cart might still be *checking* for 4.1 (or whatever the original firmware version was), in which case it would see that your 3DS has already been updated past that (therefore not invoking the update) EVEN THOUGH the actual update (if it were to be invoked) would install 9.2 on to the 3DS..
Again, I am just guessing and I don't know any thing about this stuff, but there must be a reason why the update isn't being invoked/started, you know?..