I haven't noticed a difference between any of the JSBs and FX pellets in either .22 or .25, and I think I have shot them all. Each shoots identical to their counterparts as far as accuracy/consistency is concerned...at least in my FX and Daystate guns. Only difference I see between the labels is the FX pellets tend to be noticeably cleaner in the tin and have slightly less damaged skirts. And they tend to be cheaper, surprisingly. However, I bought all of my FX pellets when they were still fairly new, so it's likely that all of mine are from "first run" batches.
What could be causing the differences that you are seeing is fluctuations between batches. The dies get both swapped out and worn as batches are run and millions of pellets are swaged. This can lead to slightly different head diameters.
Just a guess on why you may now be seeing differences. But this is exactly why when I find a pellet that a gun really likes, I then put in a bulk order to help ensure I have those same superb pellets for a looooong time. Because if I try to order them again 6 months later, they may be different.