Planes spawn to the runway with trim set as if "auto take off" is going to handle the take off controls whether you have it enabled or not. If you are well below stall speed, like when you first spawn, torque is a dominate force acting on your plane since there is not lift. Hence the aeliron will be trimmed very hard, as will your elevators be trimmed up for the slow speed.
If you are using "auto take off" the trim will balance up within a few seconds of the gear being retracted. But very rarely will "in trim" be the same as "trim centered". Except for the P-38, your roll will need trimmed off center to account for torque and p-factor.
What many players do, who want to trim manually, is also have a button set for "toggle combat trim". When you flip CT on and off briefly, it will bring the trim close to neutral (neutral not being the same as centered), and you can fine tune the trim from that point.
Other than spiking issues from your stick, I'm not seeing anything unusual with your experience. The object of your trim is to adjust so that absent stick input, your plane does not roll or pitch nose down or up. Again, usually your trim indicators will be off center when in perfect trim.