I managed to resolve the issue,
The problem was that the cut plane "Top Cutouts" was developed separately from the cutbacks on the top and bottom,

The cuts shown on the above in blue are a different feature from the purple highlighted cutout. This means that a flange can be added to the purple element when the overall cut of the profile is not 90 degrees, essentially the edge highlighted below allows it to function.

However, when the cut is 90 degrees, the two separate features become coplanar, and as far as inventor is concerned, this is the same face at the end of the profile, if this was the end of a single contour flange, or a square "cut" on the end of said flange then inventor would be able to handle it and would flange as normal as it would be formed from a single feature. Unfortunately, when creating the flange in my case, inventor sees this as a single piece of geometry as shown below but since it's being formed from two totally different features, it seems to get confused.

The solution was to add a small step to the top cutouts, This forces inventor to see this as two separate pieces of geometry and will allow the flange to be added.

This could be considered a bug in the way inventor sees profile end faces which are created from two separate features.
Intended geometry as below.
