I took over a team that had a mass exodus and I need to sign some minor league free agents to even reach my min number of players at each level of my minor league system. Ive never been able to sign guys to minor league contracts, because I get the error message that the contract will default to the minor lg min for that players experience level, even though I offer the amount in yr 1 that the player is requesting.

What can I do?

Depending on how many FA minor leaguers there are... a lot of older players that have a ML demand during free agency will simply accept a minor league role near the end of FA and during spring training.  When you assign them, it will pay them the amount for that level, I think its 54k AAA, 38k AA, 27 K for Hi, LoA.  Give that a shot.

If the FA is asking for a minor league deal, then you don't have to put anything in the year one box.  Just click "negotiate", then "submit and return".  You'll make the offer at his demand price.