I've had the same problem myself. I've got an old mini Maglite from the 80s, the old incandescent type that really eats batteries, and I wanted to put NiMH in it. Both the Eneloop and some Chinese ones I tried will not fit in. AA alkaline no problem at all. Careful measuring shows that I need to bore it out by .020" (.5mm) To make it work. But I've also got a new mini Maglite, the good LED kind, so I've not been in a hurry to chuck it in the lathe.
I also have an old AT&T model 9100 900 MHz portable phone. Yes, I still have a landline. This thing is from the mid-90s and I have had apart several times to clean the keyboard, but it is the only portable phone I've ever used which works every bit as good as a wired one. Oh yes, on to the point. The original battery pack for this phone was five AA NiCad's shrink-wrapped together with a short wire and connector that plugged into the phone. I had made a few replacement packs in the past using Sanyo NiCad, I would glue the five cells together and secure the old shrinkwrap over them with a piece of tape. That would fit in fine and beheld secure by the foam that quit the original pack from rattling. Now I use the NIMH cells, and it don't work so good. I had to take out the original foam and not use the shrinkwrap anymore, as well as making sure the wires fit down between the cells instead of under them. Even at that it requires some force to get the battery cover back on.
So basically, yes the new NIMH cells are bigger than old batteries. They may be within the official standard, but their size definitely differs from "tradition".