From your description, it sounds like you have a calculated query field that
looks something like this in query design view:
   Expr1: MyFunc([Arg1], [Arg2])

It sounds like that works without asking for parameter boxes, so I assume
that Arg1 and Arg2 are other fields in the query. But when you type
something in the Criteria row under this calculataed field, Access suddenly
starts asking for Arg1 and Arg2.

That leaves me wondering if Arg1 and Arg2 are themselves calcuated fields.
If so, you have a logical problem: Access must complete the calculations
before it can determine which records to select, but it may not be able to
perform the calculations until it knows which records are selected.

If that sounds like what you are experiencing, you might be able to solve
the problem by replacing Arg1 and Arg2 with the full expressions of those
fields instead of the alias names. For example, if the Arg1 field is:
   Arg1: [Quantity] * [PriceEach]
then you might get away with:
   Expr1: MyFunc([Quantity] * [PriceEach], ...

That will not work if Arg1 and Arg2 involve any aggregation. It that
applies, you probably need to create another query, using the existing one
as your input table. Remove the criteria from the calculated field in the
first query, and place it in the 2nd one instead.