A lot of us know what you mean, some machines do take an additional investment after the purchase cost to get them back to running like they should.
The pull handle has a latch that is unlocked by an electric solenoid, like a coil with a plunger in the middle of it. Sometimes that solenoid or the latch can get stuck or bind. You may need to examine it and clean it, looks for a loose wire connection, etc. As soon as you make the first bet the handle solenoid latch should click and release. I don't think it will be a programming or setup options thing because the SPIN button always works. You can probably remove the coin hopper and look in there on the right side of the lower cabinet to see how the solenoid locks and unlocks.
The Bally 5000 discussion area on NLG is at this link below. When starting a new discussion topic please put your initial post in this part of the forum so we won't have to move it out of the General Discussion area. That way things stay organized, it keeps all the discussion threads for Bally reel type machines together. Thanks!
http://newlifegames.com/nlg/index.php?board=75.0