Hitting 'Save' in the Add by Barcode window would save your scans. That's how you save i assume.
questions...
-are you using a scanner we offer? If not, your scanner may not be programmed correctly (possibly adding extra action as you scan).
-you scan into the 'Barcode or ISBN' field? Be sure the cursor is always active in that screen as you scan.
-have you tested if you're scanner is scanning properly? As a test, you can launch a blank text document and scan a barcode a few times to see if all the digits are being picked up with no extra spaces. If you find a problem with the scanning, try resetting back to default then reprogramming for ComicBase