Lots of variables cut out but the config and pin aliases for the relevant pins are shown

Code:
;----[18F46K22 Hardware Configuration]------------------------------------------
#IF __PROCESSOR__ = "18F46K22"
  #DEFINE MCU_FOUND 1
#CONFIG
  CONFIG  FOSC = INTIO67     ; Internal oscillator block
  CONFIG  PLLCFG = ON        ; Oscillator multiplied by 4
  CONFIG  PRICLKEN = OFF     ; Primary clock can be disabled by software
  CONFIG  FCMEN = OFF        ; Fail-Safe Clock Monitor disabled
  CONFIG  IESO = OFF         ; Oscillator Switchover mode disabled
  CONFIG  PWRTEN = OFF       ; Power up timer disabled
  CONFIG  BOREN = SBORDIS    ; Brown-out Reset enabled in hardware only (SBOREN is disabled)
  CONFIG  BORV = 190         ; VBOR set to 1.90 V nominal
  CONFIG  WDTEN = ON         ; WDT is always enabled. SWDTEN bit has no effect
  CONFIG  WDTPS = 32768      ; 1:32768
  CONFIG  CCP2MX = PORTC1    ; CCP2 input/output is multiplexed with RC1
  CONFIG  PBADEN = OFF       ; PORTB<5:0> pins are configured as digital I/O on Reset
  CONFIG  CCP3MX = PORTB5    ; P3A/CCP3 input/output is multiplexed with RB5
  CONFIG  HFOFST = ON        ; HFINTOSC output and ready status are not delayed by the oscillator stable status
  CONFIG  T3CMX = PORTC0     ; T3CKI is on RC0
  CONFIG  P2BMX = PORTD2     ; P2B is on RD2
  CONFIG  MCLRE = EXTMCLR    ; MCLR pin enabled, RE3 input pin disabled
  CONFIG  STVREN = ON        ; Stack full/underflow will cause Reset
  CONFIG  LVP = OFF          ; Single-Supply ICSP disabled
  CONFIG  XINST = OFF        ; Instruction set extension and Indexed Addressing mode disabled (Legacy mode)
  CONFIG  DEBUG = OFF        ; Disabled
  CONFIG  CP0 = OFF          ; Block 0 (000800-003FFFh) not code-protected
  CONFIG  CP1 = OFF          ; Block 1 (004000-007FFFh) not code-protected
  CONFIG  CP2 = OFF          ; Block 2 (008000-00BFFFh) not code-protected
  CONFIG  CP3 = OFF          ; Block 3 (00C000-00FFFFh) not code-protected
  CONFIG  CPB = OFF          ; Boot block (000000-0007FFh) not code-protected
  CONFIG  CPD = OFF          ; Data EEPROM not code-protected
  CONFIG  WRT0 = OFF         ; Block 0 (000800-003FFFh) not write-protected
  CONFIG  WRT1 = OFF         ; Block 1 (004000-007FFFh) not write-protected
  CONFIG  WRT2 = OFF         ; Block 2 (008000-00BFFFh) not write-protected
  CONFIG  WRT3 = OFF         ; Block 3 (00C000-00FFFFh) not write-protected
  CONFIG  WRTC = OFF         ; Configuration registers (300000-3000FFh) not write-protected
  CONFIG  WRTB = OFF         ; Boot Block (000000-0007FFh) not write-protected
  CONFIG  WRTD = OFF         ; Data EEPROM not write-protected
  CONFIG  EBTR0 = OFF        ; Block 0 (000800-003FFFh) not protected from table reads executed in other blocks
  CONFIG  EBTR1 = OFF        ; Block 1 (004000-007FFFh) not protected from table reads executed in other blocks
  CONFIG  EBTR2 = OFF        ; Block 2 (008000-00BFFFh) not protected from table reads executed in other blocks
  CONFIG  EBTR3 = OFF        ; Block 3 (00C000-00FFFFh) not protected from table reads executed in other blocks
  CONFIG  EBTRB = OFF        ; Boot Block (000000-0007FFh) not protected from table reads executed in other blocks
#ENDCONFIG

#ENDIF

;----[Verify Configs have been specified for Selected Processor]----------------
;       Note: Only include this routine once, after all #CONFIG blocks
#IFNDEF MCU_FOUND
  #ERROR "No CONFIGs found for [" + __PROCESSOR__ +"]"
#ENDIF


DEFINE  OSC 64             ' Int Osc (16MHz + 4*PLL)
DEFINE  ADC_BITS        8  ' Set number of bits
DEFINE  ADC_CLOCK       3  ' Set clock source 
DEFINE  ADC_SAMPLEUS    50 ' Set sampling time 
'DEFINE  HSER_SPBRG 9   ' 250 KBaud 
define  HSER_BAUD 9600
DEFINE  HSER_CLROERR 1 ' Clear overflow automatically
define  SHIFT_PAUSEUS 50 ' Speed of shiftout

' **** Define LCD Config ****
DEFINE LCD_DREG    PORTD        ' LCD is connected to Port D
DEFINE LCD_BITS    4            ' 4 bit mode
DEFINE LCD_DBIT    4            ' Connected to D.4-D.7 
DEFINE LCD_RSREG   PORTC        ' RS pin is on Port C
DEFINE LCD_RSBIT   4            ' RS = C.4
DEFINE LCD_EREG    PORTC        ' Enable on Port C 
DEFINE LCD_EBIT    2            ' Enable = C.2
DEFINE LCD_COMMANDUS 2000       'Command delay time in us
DEFINE LCD_DATAUS  200          'Data delay time in us

INCLUDE "DT_INTS-18.bas"       ; Base Interrupt System
INCLUDE "ReEnterPBP-18.bas"    ; Include if using PBP interrupts
INCLUDE "Elapsed_INT-18.bas"   ; Elapsed Timer Routines


OSCCON = %01111000  ' Set to 16MHz Internal Oscillator
OSCCON2 = %10000100
OSCTUNE = %01000000

TRISA = %00001111		
TRISB = %11011111
TRISC = %11000000
TRISD = %00000000
TRISE = %00000000

PORTA = %00000000
PORTB = %00000000
PORTC = %00000000
PORTD = %00000000
PORTE = %00000000


ANSELA = %00001111  ' AN0-AN3 enabled as Analog Inputs
ANSELB = %00000000  ' Disable Analog Inputs
ANSELC = %00000000  ' Disable Analog Inputs
ANSELD = %00000000  ' Disable Analog Inputs
ANSELE = %00000000  ' Disable Analog Inputs

ADCON0=   %11000000
ADCON1=   %00000000
ADCON2=   %00000110       
CM1CON0=  %00000000


NeoPin        var LATB.5   'NeoPixel Pin
APAData       var LATE.1
APAClock      var LATE.0
It works with APAData and APAClock on Port E but when they are on LATA.7 and LATA.6 then NeoPin stops working