Hi Jason,
"I have processed an image and it look good. I can save the file with as .fit, but when I re open the file the sceentranfer appears to have gone. (the image is pretty much dark as the raw file, only showing a few birght stars and need to use screen tranfer again). Is there a way to save the image as i saved it after processing?"
Screen Transfer Function works only for visualization. So, STF doesn't affect the image process. You should use Histogram Transformation: once used STF, reset it and use HT. You can use the same parameters you've got with STF by dragging the 'execute' icon of STF into Histogram Transformation window (into the lower edges, beside 'execute' and 'apply' icons). Then, execute the action in your image with HT.
"And also I am trying to save the file as a .jpg, but i keep getting the warning that the format is not supported and some data will not be saved. When i save it and open the .jpg file it also looks very dark only showing a few bright stars."
Don't worry about the warning message if you have a master image copy in 32bit FIT. The message warns you that the sample data will change to a lower bit sample. You'll see how JPEG has less accuracy. But it doesn't changes your process. Also, other message warns you about FITS keywords data won't be saved.
Hope being helpful,
Marc