I've had some minor misalignment on some boards I've done. It is frustrating...
My solution was to proceed with the glue up, aligning the strips visually, there will be some slight misalignment, try rearranging strips to help, don't worry about edge alignment as you will trim all edges equally to fix that.
Once the board is done, you will barely notice the issue, and only you will notice it, everyone else will remark how gorgeous the piece is!!
You do obviously have an issue somewhere that is causing this, only way to figure it out is to get out a pair of calipers and check each operation.