Do the volume buttons control your amp or your speakers? If the following does not solve your problem, tell us what model of each you have.
Did you learn the volume commands? If so, relearn them and hold the button on the original remote down until the 3000 beeps.
That should work, but if it doesn't, try a short press and see what happens.
When taking the batteries out, you must leave them out at least 20 seconds before putting them back in or you will lose all your settings.
These threads will answer your questions, and others which may arise.
RM-AV3000/3100 NEWCOMER’S PACKAGE-WELCOME-CHECK THESE OUT (IF YOU HAVEN’T ALREADY DONE SO) AND SAVE YOURSELF SOME PROBLEMS AVOID SYSTEM CONTROL PROBLEMS HOW TO LABEL, CHANGE OR HIDE BUTTONS CHANGING BATTERIES (May not apply to RM-AV3100-time will tell)