"They" are Bic Camera and Yodobashi Camera, the two main electronics/camera/film stores in Japan (here). I know it's C-41, but they claim they "have to" send it to Kodak. I've heard stories of people with better japanese language skills than mine managing to convince the odd guy at the counter to process them together with the rest of their color negs, but it seems to be rare & difficult (pro labs like Horiuchi are apparently more easily convinced, but they're also more expensive than big stores).
I doubt it has to do with the scans or prints as I never order either of these (I scan everything myself, their scanning service is expensive and relatively low-res). i wish I could develop myself, but it's not an option where I live currently. Maybe in the next apartment...
I'm not shocked by this. Any subroutine out of the ordinary can, I've found, throw staff for a loop. I'll never forget my visit to Tokyu Hands when I presented the writing pen specialist with one of my venerable Pilot BP-S ball-point pens that I've used for over 25 years. They are made in Japan by a Japanese company. The look on his face, though, was of abject confusion. Rather than just shaking his head indicating that they did not sell it, he looked at the pen, then at his display, puzzled, then around the display, then to another co-worker in the writing pads area, who also looked confused, and then he ambled back to me. It was as if I'd presented him with a steak knife or something completely of a different nature like I had somehow short-circuited something. My travel partner, a former resident, explained the whole breaking-routine-causes-confusion response dilemma.
In short, the suggestion I might offer is this: circle "C-41" on both a roll of Fujicolor and the roll of Ektar and make a point to note they are one in the same. It might not work, but being as literal as that is nevertheless worth a try.