Apologies for dragging up an old thread but I found it while searching the forum for info on the problem.
I'm using an Ixus 980IS (SD990) with the 1.00e build. I've been experiencing the problems with RAW files being sporadic too.
For me, shooting in P mode, it seems I have no problem with the flash switched off but I do need to use the half-press, pre-focus in order to get the RAW file written. Simply pressing the shutter release quickly results in only the .jpg getting written.
Hope this helps in development.