So I minimized the code:

Code:
asm
 __CONFIG    _CONFIG1H, _FOSC_INTIO67_1H & _PLLCFG_ON_1H & _PRICLKEN_OFF_1H & _FCMEN_ON_1H & _IESO_OFF_1H
 __CONFIG    _CONFIG2L, _PWRTEN_ON_2L & _BOREN_SBORDIS_2L & _BORV_285_2L
 __CONFIG    _CONFIG2H, _WDTEN_OFF_2H
 __CONFIG    _CONFIG3H, _CCP2MX_PORTC1_3H & _PBADEN_OFF_3H & _CCP3MX_PORTE0_3H & _HFOFST_OFF_3H & _T3CMX_PORTB5_3H & _P2BMX_PORTC0_3H & _MCLRE_EXTMCLR_3H
 __CONFIG    _CONFIG4L, _STVREN_OFF_4L & _LVP_OFF_4L & _XINST_OFF_4L & _DEBUG_OFF_4L
endasm

DEFINE OSC 16
OSCCON  = %01010000
'     R/W       111 = HFINTOSC – (16 MHz)
'               110 = HFINTOSC/2 – (8 MHz)
'               101 = HFINTOSC/4 – (4 MHz)

OSCTUNE = %11000000
OSCCON2 = %00000100
INCLUDE "DT_INTS-18.bas"
INCLUDE "ReEnterPBP-18.bas"
INCLUDE "Elapsed_INT-18.bas"
ASM
INT_LIST  macro    ; IntSource,        Label,           Type,   ResetFlag?
        INT_Handler   TMR1_INT,   _ClockCount,   PBP,  yes
    endm
    INT_CREATE
ENDASM
ANSELA = %00000000
ANSELB = %00000000
ANSELC = %00000000
ANSELD = %00000000
ANSELE = %00000000
ADCON0 = %00000000
TRISA = %00000000
TRISB = %00000000
TRISC = %00000000
TRISD = %00000000
TRISE = %00000000
PORTA = %00000000
PORTB = %00000000
PORTC = %00000000
PORTD = %00000000
PORTE = %00000000
    pause 100
@ INT_ENABLE  TMR1_INT 
    GOSUB ResetTime
MainProgram:

    if T1CON.0 = 0 then
        PortD.3 = 1
        GOSUB StartTimer
    endif

    if ticks = 5 then
        PortD.3 = 0
        GOSUB StopTimer                    ' Stop the Elapsed Timer
        GOSUB ResetTime                     ' Reset Time to  0d-00:00:00.00
    endif

    goto MainProgram
end
5 TICK Timer

OSC 16MHz (4MHz+PLL) 50ms
OSC 32MHz (8MHz+PLL) 25ms
OSC 64MHz (16MHz+PLL) 12.5ms

I can't help but feel I'm doing something wrong, it's just too proportional a variance. If the Saleae probe would miss pulses, there wouldn't be a regular pattern.