This may occur when the invoices have different post statuses. When processing checks through Print checks and Record Bank Drafts, one of the options for post status is "From Invoice".  When this option is selected, the payment's post status must mirror that of its invoice. Thus, if two invoices are to be paid, and one is Not Yet Posted and the other is set to Do Not Post, two checks will be created to ensure that each check reflects the related invoice's post status.

To override this, it's possible to set the Post Status option in Create Payments to "Not Yet Posted" (or Do Not Post). Once set, all invoices will be paid with the same check.