Back to cooking with gas........
Code as was before:
Code:
'MRF initialization here
debug "@ MRF init", 10
            MRFConfigSel=0                                                      'Select the chip       
'Going to try using shiftout before using hardware SPI
            for i=0 to 31                                                       'Sets up the index var for data
                MRFaddr=(i << 1)                                                'Shifts address 1 bit to left, automatically gets start,write, and stop bits      
                SHIFTOUT SDO, SCLK, 1,[MRFaddr,RF_Init_Values(i)]               'send data to register
debug "Addr=",bin8 MRFaddr,"  Value=",hex2 RF_Init_Values[i],13
            next i    
            MRFConfigSel=1                                                      'Deselect the chip

'Try to read back some registers as a test to see if they were written correctly            
            MRFConfigSel=0                                                      'Select the chip 
            for i = 0 to 7                                                      'Sets up address to read
                MRFaddr=((i << 1) | $40)                                       'Shifts left 1 bit, sets $40 bit, automatically gets start, READ, and stop bits
                SHIFTOUT SDO, SCLK, 1,[MRFaddr]                                'Address to read
                SHIFTIN SDI, SCLK, 0,[MRFSPIdata]                              'Get data from reg
                debug "MRF Config data: i=", dec1 i, "   Register ", bin8 MRFaddr, "   Data=", hex2 MRFSPIdata,13
            next i
And the debug output:
Code:
@ MRF init
Addr=00000000  Value=28
Addr=00000010  Value=8C
Addr=00000100  Value=01
Addr=00000110  Value=63
Addr=00001000  Value=0C
Addr=00001010  Value=03
Addr=00001100  Value=77
Addr=00001110  Value=64
Addr=00010000  Value=32
Addr=00010010  Value=74
Addr=00010100  Value=62
Addr=00010110  Value=32
Addr=00011000  Value=38
Addr=00011010  Value=00
Addr=00011100  Value=19
Addr=00011110  Value=00
Addr=00100000  Value=A3
Addr=00100010  Value=38
Addr=00100100  Value=30
Addr=00100110  Value=00
Addr=00101000  Value=00
Addr=00101010  Value=00
Addr=00101100  Value=53
Addr=00101110  Value=59
Addr=00110000  Value=44
Addr=00110010  Value=00
Addr=00110100  Value=70
Addr=00110110  Value=BC
Addr=00111000  Value=02
Addr=00111010  Value=01
Addr=00111100  Value=5E
Addr=00111110  Value=00
MRF Config data: i=0   Register 01000000   Data=28
MRF Config data: i=1   Register 01000010   Data=8C
MRF Config data: i=2   Register 01000100   Data=01
MRF Config data: i=3   Register 01000110   Data=63
MRF Config data: i=4   Register 01001000   Data=0C
MRF Config data: i=5   Register 01001010   Data=03
MRF Config data: i=6   Register 01001100   Data=77
MRF Config data: i=7   Register 01001110   Data=64
Which matches perfectly.

I did scope the data in, out and noticed the pulses were not right at all.
Then double-check the schematic and board to the datasheets - cuz, you know sometimes there is a mistake.........
I appreciate your help, your going back to basics post was done after I had done it so we think alike - I am just DUMB!

Your help in finding the correct way to address the registers was of immense help, I just missed that one completely.
I'm off to the races, well, off to get the code for a wireless smart sensor system for the house.......
When working, will post code to help others.

Regards.