If the yellow and green LEDs are blinking at one flash each simultaneously, it indicates that the acceptor has been disabled by the machine interface.
Had one on an S2000 that did that. I went into the configuration menu and enabled it, then ran Netplex Auto Config and it solved my problem.
Not sure how the Bally Alpha menus are set up, but you can look around and see if anything catches your eye.
Or it could be a bad MEI head, Interface Card or Cash Can. I've had some that were flashed only to accept tickets, not bills. That drove me crazy figuring that out.
Same thing though, bezel lights on, sucks in bill, spits it right back out.
Good luck, if you have a different head, card and cash can, start doing some swapping until you find a combination that works.
Curtis ash100