I write or modify the code locally, ctrl-S (save) ctrl-A (select all) and then ctrl-C (copy). I then switch to the web browser (Firefox 2.0.0.14 usually but that doesn't seem to be relevant) and ctrl-V (paste) into the web page and save using drupals save function.
Almost every time I switch back to Rapid PHP, I get the dialog box stating "Another application has modified ... Do you want to load the updated version?" which has to be clicked on to clear it.
There is no link whatsoever between the two (FTP or otherwise), nor am I changing the file locally in any way that I know of.
I have copied the original saved file before clicking the upload box to compare the two versions and they appear identical.

