Hi David, your best bet is to use 123Scan to modify the output by stripping the CTRL-D.
I note the 1D barcode is Code 128 and produces SBR81201902.
The 2D barcode is PDF-417 and is more complex.
[)><RS>06<GS>1P1/BFL 901 009/1<GS>21PR3B<GS>22PSUP 6601 <GS> 12D20110215 <GS> SBR81201902 <RS> <EOT>
<RS> = record separator, ASCII 30 or CTRL-^
<GS> = group separator, ASCII 29 or CTRL-]
<EOT> = end of transmission, ASCII 4 or CTRL-D
So the <EOT> in the 2D barcode is the problem as you say.
So using 123Scan create a configuration for your scanner. Within the config section select Modify Data and then choose Program complex data modification / Advanced data Formatting / Create a New Rule. Since I am not sure what other barcode you scan it is hard to give exact instructions from this point on but suggest you create a rule that only works on PDF-417 barcodes and program it so it drops the last character.