I went back to my Game Controllers under Control Panel in Windows, and I had added a joystick called "Special" because of the calibration problem. Don't ask me why that works, but that is what MS told me to do back when I had trouble. The elevator position has an indicator on the FS98 control panel which should be centered with you hand off the joystick. Is yours? If it is full up with the joystick activated then you know you have a joystick or calibration problem.
The joystick works fine on FS98 airliners, but I find control is easier with the keyboard. It is easier to hold the pitch steady when all you do is punch keys when you want it to move, whereas a joystick will move the elevators everytime you move your hand. But I cannot fly a fighter with a keyboard because that is not responsive enough for quick manuevers. Heavy jets don't do quick manuevers. This is, of course, personal preference.
They sell control yokes with throttles which would be a better imitation of a 737 (for example) but I've never invested in one of those.
Hope you get your joystick working. Remember I am lucky to find the "on" switch on a computer, and take whatever I tell you as names of these functions with a grain of salt (look around and find something similar to my names).