Arduino Mega, PWM analogWite doesn't work with Timer interrupt
When you use a timer to generate an Interrupt Service Routine (as you do with the TimerOne library) you change the configuration of that timer (in your case timer1). The timer is used by the TimerOne library to provide an interrupt, but also by the microcontroller itself to produce a PWM signal on some pins depending on the timer: in your case (Arduino Mega, timer 1) on the 11 and 12. If you use one of these pins as "analog" output while controlling an ISR with the same timer you won't get the expected output, because the timer isn't any more configured as needed by the PWM generation mechanism but as needed by you (you changed the configuration of the timer in the Timer1.initialize(100000); function call).



So, either you use another PWM pin as output either you use a timer library which uses another timer (or you implement it by yourself).