I added the port configuration and acon register configs. That has an effect...
The bootloader never leaves the bootloader mode to run the user app.

if I comment out the Hardware configuration section and compile I can load the code via the bootloader, the device disappears from the USB list and then ~10seconds later I get the USB device not recognized.

I have reloaded the led test program just to make sure the bootloader and chip are still working and they are. Very puzzling, but the registers do seem to have an effect.

Nothing in the DT_INT writes to EEPROM 0x00? If there is a 5A there then the bootloader thinks its still in boot mode.

Code:
    LED1   VAR  PORTB.0
    
    DEFINE OSC 20          
    DEFINE RESET_ORG 0x800  
    
    INCLUDE "DT_INTS-18.bas"        ' Base Interrupt System
    INCLUDE "ReEnterPBP-18.bas"     ' Include if using PBP interrupts                                           

    '   Hardware configuration
    '   ======================    
        '
        '   I/O and PORTs
        '   -------------  
    PORTB   =   0
    PORTC   =   0
    PORTD   =   0
    PORTE   =   0
    TRISB   =   %00000000       '<2-1> Inputs
    TRISC   =   0
    TRISA   =   0
    TRISD   =   0
    TRISE   =   0
        '
        '   A/D converter
        '   -------------       
    ADCON0  =   %00000000       ' A/D converter off     
    ADCON1  =   %00001111       ' All Digital Inputs
 '   ADCON2  =   %00000000 
                           


ASM
INT_LIST  macro    ; IntSource,        Label,  Type, ResetFlag?
        INT_Handler   TMR1_INT,  _ToggleLED1,   PBP,  yes
    endm
    INT_CREATE               ; Creates the interrupt processor
ENDASM    




T1CON = $31                ; Prescaler = 8, TMR1ON
@ INT_ENABLE  TMR1_INT     ; enable Timer 1 interrupts

Main:
    Pause 10  
GOTO Main

'---[TMR1 - interrupt handler]--------------------------------------------------
ToggleLED1:
     TOGGLE LED1
@ INT_RETURN
Still puzzled...