Pixel is not a measurement unit of length per se.
If a screen has more pixels per unit of length an image (when displayed as one image pixel per one screen pixel) would appear smaller than on a screen with lower resolution.
To make sure could you please post an image that is 500px x 500px (according to Image > Image Size) but seems to be too small to you?
Sounds to me that this is to do with a retina display (2x)???
What system are you working on?
I remember a thread where a poster with a high resolution screen claimed an image was not displayed correctly (with regard to size) and posted a screenshot that clearly indicated it was …
And it seems to be the same here; when measuring the white rectangle/canvas in the image "1416948490-ScreenShot-o-1 copy.png" it is 500px by 500px.