Hi, In many programs, you can save content to different file types. For example in Paint, you can save the image as a jpeg, bmp etc. Soundshaper doesn't as yet do this sort of conversion when saving (exporting) files. So if the output type is .wav you should select .wav as the file type, if .ana, select .ana and so on. The message you quote comes up only if you're trying to save the output file to a different type. This applies to saving via the standard Windows selector and the SAVE box on the left. The output cell is colour-coded to help with file-types: white for wav soundfiles, aqua for spectral freq. files (.ana), mauve for pitch-data files (.frq), green for formant file (.for), red for binary envelope files (.evl), plus a few others.
There is one exception to the above, though. If Option 5 ("Auto-FFT ana-wav") is set (and I think it normally should be), spectral output (ana files) are auto-converted to .wav for play and display purposes (although aqua for ana is still the cell-box colour). You can therefore select .wav as the output file-type to save to. Soundshaper does have a range of auto-conversions and maybe more should be applied when saving (I'll look into this), but some are not technically possible anyway, e.g. .for to .wav. It would be clearer if the file-types listed for saving could be narrowed to show only the relevant ones and I'll look into that for the next update.
You're welcome to send me any screenshots if this doesn't help. I'm not clear what you're referring to when you "open up windows to do processing it looks well out of whack" - maybe a screenshot would help here.
Robert