EDIT - Disclaimer: I would like to refer the readers to the discussion with ChrisW below. It might be that getting an area based upon an OTF CRS is not a bug after all; that is, at least, in arcgis it also being used to allow geoprocessing two layers from different CRS.
To elaborate on the issue above. As AndreJ as suggested and show - this is probably a bug in qgis's current version. Yet it should be noted that the problem isn't the wrong area, but that on-the-fly transformation affects in anyway on area calculations.
The purpose of on-the-fly transformation/projection is to align data from different sources and with different CRS. That is mainly for display purposes. E.G. arcmap automatically perform on-the-fly projection in any case a layer CRS does not match the data frame CRS.
Arcmap also provides a possibility to edit data while projected on-the-fly, but also notes that: (source)
However, it is important to note that certain editing operations may produce unexpected alignment or accuracy problems, depending on the coordinate systems being used.
Specific editing operations that may cause issues include changing the shapes of features, snapping to the edge or boundary of features, or extending and trimming features. These problems are more likely to occur when the features you are editing are close to the edge or beyond the area of use of the coordinate system
That is to say: on the fly transformation is less acurate than just project the data to a different CRS (which also introduces its own problems).
Having said that it is not surprising that based on a on-the-fly transformation a wrong area is being calculated, yet it is surprising that the fact that on-the-fly was enabled affects in any way the calculation of geometry, which should be based on the data. Thus, it doesn't matter if on-the-fly transformation is based upon the same or a different CRS, area calculation should be identical each time.
To be more practical, if your aim is to compute the area do not use on-the-fly. If you have the wrong CRS, project your data.
Best Answer
From what I understand about QGIS, changing the CRS on a layer is not the same thing as projecting to a new CRS. If you have a layer with X Y defined by latitude and longitude, and then just change the CRS to a projected coordinate system, the X Y values do not change. Basically it takes those latitude and longitude values and interprets them in terms of units of the projected CRS that you changed to, so everything will be completely messed up like you are seeing.
If you just want measurements in EPSG 2264 you can change the CRS of your map by selecting the button in the lower right of the screen. When selecting your CRS check the box at the top that says "Enable 'on the fly' CRS transformation (OTF)."
This will keep your layer in 4269 like it should be and transform it to 2264 so that your measurements in the map are in ft.
If you really want to change your layer, I think if you do a save as, and select 2264 as the CRS it will transform your layer and save it with the new CRS.