Different springs will give different results, if you get two springs that are both exactly the same, you've already had a miracle.
I have a .22 99s myself, tried wth different springs but always the same piston/piston seal, with the harder spring, they were all closer to 11 fpe, with the softer Titan No. 10 spring it gave different results altogether, I aimed to set it around 11 fpe, it came out at 11.3 with Exacts and RWS superfields,both 15.9 grn , it was only about 10.4 with the lightweight RS 13.4 grn but the Superdomes came out around the 11.9 mark 14.6 grn , so I reduced it a little bit to stay in safe limits, but the Supedomes are the middlewieght of all the pellets , but make the most power by quite a bit from all of them. I wouldn't worry if you get such variations , just stick with the most accurate pellet in that barrel, just make sure no other pellet can take it over the limit and don't worry about all the figures , accuracy is what you are after, if you hunt ? A rabbit would not know the difference between a 10 fpe gun and a 11.5 fpe gun, where you aim and hit is the main concern. My gun would actually produce a 3fps spread with superfields, but they weren't as accurate as some of the other pellets .
Probably all down to your barrel, how it likes certain pellets and how the spring sends that air pulse down the barrel when you fire, harder faster spring sending the pellets off quicker than the softer spring that catches up with itself later in the firing cycle .