When you steep grains, that is specialty grains where the starches has already been converted into sugars, BeerSmith applies a "steeping efficiency" of (I think the default is) 19%, which is to say that 19% of the potential of the specialty grains becomes added to the gravity of the wort being produced.
When you have a base malt, such as wheat malt in your example, the enzymes released will convert any starches into sugars for the yeast to consume. This is a much more efficient process at delivering fermentable sugars. When this happens, the type of recipe should be changed to 'partial mash' to accommodate the increased sugars being liberated. Here BeerSmith uses your brew house efficiency to figure out how much sugar needs to be extracted from the mash and calculates a mash efficiency based upon the percentage of the grain potential which is utilized.
So for your recipe, carapils is a dextrine malt which does not need to be converted and can be steeped to release the sugars it contains. When steeped (at least in my experience) much of the dextrines seem to be reduced by the available enzymes into fermentable sugars.
Malted wheat is a base malt which is composed of starches only, but also contains enzymes which will act to reduce those starches into sugars when mashed (steeped) at temperatures between 145?F and 162?F.
Flaked wheat and flaked oats are unconverted grains which have starches but no enzymes to reduce those starches to sugars. As such, to realize any amount of sugar potential from them, they must be mashed with an enzymatic base malt (such as the malted wheat.) Putting them into a recipe with no base malt will release some starches into your wort, but no sugars. These starches will not be used by the yeast, but can be consumed by other bacteria, leading to a reduced shelf life of your beer.
The net result for you is 'yes' you were doing a partial mash (you had unconverted grains and 'steeped' with an enzymatic base malt), and that explains the increased gravity you realized from these batches. If you look at the description of these malts in BeerSmith, you will find that some of them are marked "TRUE" for the 'must mash' descriptor. Those are malts that need to be mashed in order to contribute fermentable sugars. Those malts that are labeled 'TRUE' for the 'must mash' descriptor and have a value above zero for 'diastatic power' are base malts which have some enzymatic potential to provide those enzymes needed to reduce the starches to sugars for the yeast to feast upon.