Hi Pam,
The new batteries should work right away. (Your old ones had gone solid from sitting for so long- charge the new ones at least once a week to keep that from happening, even if you are not using your power chair.)
You may want to check all of the connections to make sure they are tight especially on the battery posts, also make sure the fuses are not burned out. It's recommended to run the new batteries into the red (fully discharge) then let them charge for 8-12 hours to make sure the batteries get a full charge the first time out, but if you haven't done that, it should not cause any flashing lights.
You said that green lights were flashing (assuming on the controller); if all 10 bars (3 red, 4 yellow, 3 green) are flashing that indicates a poor battery connection. 9 bars means you need to do a brake reset. Check page 51 of your manual for controller light codes or check this link:
http://www.pgdt.com/scenter/diagnostics/diagvsi.html
If you have any other concerns, let me know. Good luck!
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