Hi William this is from one of my posting about setting the bit to a kreg jig. This is the method I use and it has never failed me. Refer to my post in April 2011 for more and it was in reply to splitting face frame joints.
I started using the kreg jig at the start of it introduction on to the market, having one of the first jigs sold which was the K2 model. At that time there was no build in guages and or other devices for setting the debth collar on the drill bit. To make it easy and simple the use of a american coin the nickel was the best method I could find to set the debth collar. I had two reasons for this as it kept the drill bit from hitting the base on the jig but also prevented the bit from exiting the hole on the piece that you were going to attach the drilled piece to. The exiting of the screw left a small dimple at the exit and was a protrussion that prevented a tight connection of the wood. I have mulltiple jigs now and still use this method as an assurance to proper setting of the bit. I have about 20 years building cabinets and custom wood work as a profession and this method of setting the bit has never failed me . Ref to photo. If you do not have the type with a base on it similiar to the one below it will not apply and you will have to refer to the instruction sheet that came with the jig. hope this answers your question.
William, your 1 1/4" screws are the correct length to join 3/4" boards, it sounds like you have not set the Kreg Jig up correctly,
When you set your depth collar you need to set it where the step on the drill bit is on the correct mark (in your case 3/4") and not the tip of the drill bit.
I would also recheck to make sure that your drill guide on the kreg jig is set to the correct mark (in your case 3/4")
Hope this helps.