Microcontroller input state counter problem - c

Question

I am doing a major embedded project of making a GM counter. As a main microcontroller I am using a PIC32MK1024MCM064. I wont bore you with details, but I need to implement following algorithm:
When MCU turns on, 13 seconds delay has to pass
MCU waits for a button press, which triggers an interrupt
Button interrupt starts 60 seconds timer
During that 60 seconds, MCU input pin counts the impulses (Idle voltage state is high (3.3V) and low voltage state counts as an impulse (50-130 us duration))
After the timer has expired, MCU outputs the impulse number via 16x2 LCD screen
Project has many files included in it, but I have already verified all the peripheral code is written right:
I have already made sure, that my button interrupt and the timer interrupt work absolutely fine (used the oscilloscope, real timer and all the other stuff.)
I also verified that my I2C driver for the LCD screen works great as well.
I made sure I am indeed getting the low state impulses as defined (50-130 us duration.)
#include <xc.h>
#include "configurations_bits.h"
#include <stddef.h>
#include <stdint.h>
#include <stdbool.h>
#include <stdlib.h>
#include "stdio.h"
#include <sys/attribs.h>
#include "delay.h"
#include "inter_integrated_circuit_protocol.h"
#include "liquid_crystal_display.h"
#include "pulse_width_modulation.h"
#include "timer.h"
#include "state_change_interrupts.h"
static int Particle_count = 0; //Variable for counting events
char Value[10]={0}; //Particle value string
int main(void) {
__builtin_disable_interrupts(); //Global interrupt disable
ANSELA = 0x00000000; //Enable PORT A digital inputs
ANSELG = 0x00000000; //Enable PORT G digital inputs
TRISEbits.TRISE12 = 0; //Output gpio of a led
TRISDbits.TRISD8 = 0; //Output gpio of a led
TRISGbits.TRISG9 = 0; //Output GPIO of GM ENABLE
LATGbits.LATG9 = 1; //Enable GM right away
TRISAbits.TRISA1 = 1; //Input for counting particles
TRISCbits.TRISC7 = 1; //Input for control button
Inter_Integrated_Circuit_Setup (); //I2C configuration
Inter_Integrated_Circuit_Enable (); //I2C enable
Liquid_Crystal_Display_initialization(); //LCD configuration
Liquid_Crystal_Display_Set_Cursor(1, 1);
Liquid_Crystal_Display_Write_String("Preparing for");
Liquid_Crystal_Display_Set_Cursor(2, 1);
Liquid_Crystal_Display_Write_String("Measurement");
Pulse_Width_Modulation_Setup(); //PWM setup
Pulse_Width_Modulation_Enable(); //Turn on high voltage generation
for(int i=0; i<13; i++){
delay_ms(1000);} //Waiting until the high voltage rail rises up to 400V (starting GM tube voltage)
Liquid_Crystal_Display_Clear(); //Clearing LCD
Liquid_Crystal_Display_Set_Cursor(1, 1);
Liquid_Crystal_Display_Write_String("Ready for");
Liquid_Crystal_Display_Set_Cursor(2, 1);
Liquid_Crystal_Display_Write_String("Measurement");
State_Change_Interrupts_Setup (); //Button interrupt setup
Timer2_Setup (); //Timer interrupt setup
__builtin_enable_interrupts(); //Global interrupt enable
while (1){
if(T2CONbits.ON){ //Condition, that the timer is on
Liquid_Crystal_Display_Clear(); //Clearing LCD
Liquid_Crystal_Display_Set_Cursor(1, 1);
Liquid_Crystal_Display_Write_String(" Measurement Is ");
Liquid_Crystal_Display_Set_Cursor(2, 1);
Liquid_Crystal_Display_Write_String(" In Progress ");
while(T2CONbits.ON){ //Execute this while cycle until the timer shuts off
if(PORTAbits.RA1==0){
Particle_count = Particle_count+1;
delay_us(100);} //GM tube dead time compensation
}
Liquid_Crystal_Display_Clear(); //Clearing LCD
sprintf(Value,"%05d CPM",Particle_count);
Particle_count=0; //Resetting the CPM value
Liquid_Crystal_Display_Set_Cursor(1, 1);
Liquid_Crystal_Display_Write_String(Value);//Printing radiation level in CPM notation
delay_ms(5000);
Liquid_Crystal_Display_Clear(); //Clearing LCD
}
}
return (EXIT_FAILURE);
}
When I press the button, my LCD outputs "Measurement Is In Progress" for a fraction of a second, then it immediately outputs "00000 CPM" which means it had counted zero impulses (In my application, I know for sure that I must capture at least 5 impulses per minute.) Looks like the while cycle has only one or few iterations (it should last for a minute). So my code problem is not a missing semicolon somewhere, but I feel like the whole architecture is not right. Have you got any observations or suggestions, how could I implement the mentioned algorithm? Want to thank you in advance.
(P.S I am running a 8 MHz internal FRC as the main clock)