Brian - I can only speak to Canon's implementation - and yes there is still a pre-flash if the camera is set to manual exposure and flash is set to ETTL. If the flash is set to manual then there's no pre-flash. How else is the system supposed to know how much power the flash should be set at? So yes, flash exposure is adjusted when using manual exposure - at least with Canon. The flashes are very quick but they're there. Again, remember we're talking camera in manual not the flash.
Now, it may very well be that Pentax uses a different approach that has no ability to adjust flash output when camera is set to manual. That would be unfortunate. It's relevant if the OP is using Pentax.