I think I know what I am doing wrong....the DPI needs to be at 72 to be 3 x 3, however I have to make it 300 for my project, and when I do that, the working area increases by like 3 times.
Is this project going to be used for a print job or web? You need to set it up correctly when you create the file based on what it will be used for.
If print, then set it to the size in inches for the size it will be printed: 3 in X 3 in, and you should use at least 300dpi - if your machine can handle it, resolutions as high as 1200dpi will look even better in print.
If this is a web project, the dpi is completely irrelivant, it will be whatever the end user's screen is set to. Do not set the size in inches, just whaver pixel size will fit on the page. So for 3"x3"x72ppi you want to set the file to 216px X 216px.
I'm not sure why the file might change itself after it was saved and re-opened. Keep in mind that as long as you end up with the same number of pixels in the end, it probably doesn't matter. 3" x 3" @ 900dpi = 9" x 9" @ 300dpi = 2700px X 2700px. So as long as you end up with the same either way, the printer can probably sort it out just fine.