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For a home machine that has the ability to have its credits denominated in different amounts many people like to set it to the lowest denomination so that when they insert a bill the machine will give them a lot of playing credits, makes it easier and faster to put credits on the machine instead of inserting bill after bill. It sounds like maybe your machine was setup this way. Even though it is a nickel machine, it is setup for 1 credit = 1 cent. So when you insert a $1 bill you get 100 credits. It will still payout from the hopper in nickels since that's how the hopper is setup. This denom amount can be changed if you want, but realize you'd then have to insert many bills to get the same number of playing credits.
Here's a page from the Bally 6000 manual, it looks like Dipswitch DS2, switches 1,2,3,4 set the denomination. You can check yours to see if it matches the table below before changing anything. If I am reading this correctly you need to change Dipswitch DS2, switch 1 from OFF to ON to switch it from penny to nickel denomination. Be sure to do this with power turned off. I think this will change things so you get 20 credits when $1 bill is inserted.