Accoring to the user manual on page 19, the battery icon flashes for two reasons - (1) when the battery power is low, and (2) when the internal battery charge circuit is active.
In the original poster's case, the battery icon is flashing because the internal battery charge circuit is active. The user manual says "Your scanner provides an indication when the the internal battery charge circuit is active. The battery icon briefly flashes approximately once every second". It also says, "The battery charge indicator does not provide positive indication that the batteries are actually being charged. Batteries will not charge unless the yellow battery holder is used".
What the user manual doesn't say is that there is actually a way to turn the internal battery charge circuit on and off while the scanner is plugged into the wall. To do this, go to ....
PGM - GLOB - Battery Info - Select
You will have three options to control the internal battery control circuit:
Done - Do nothing and return to previous menu item.
Stop - Stop the internal battery charging circuit.
Reset - Reset the internal battery charging clock and continue charging.
Charg - If the internal battery charging circuit is already off, you will have this option to turn it back on.
Revised to add - These options will not be available if the scanner is not plugged into the wall and is running on battery power.