I have had this with an IB-1 kit. I got over it by using a Dremel with a drum sanding wheel and running it around the input jack hole.
This will only get you 1/3 or 1/2 way in to the hole's depth though. For the deeper part I had to run around the hole with a round file, kinda like draw filing in a circle, this got me enough space to be able to get the jack all the way into the hole. Depending on the type of jack used, you may need to cut the rubber washer that sits behind the flange down to the same diameter as the flange. Either that or you continue to sand/file out until you can clear both.
You need to be really careful either way, it is very easy to distort the sharp edged form of the hole and once it becomes irregular, it would be a bugger to try and get it back to a uniform oval opening.