slidecast synch waveform not synched

I just created my first slidecast and overall I'm quite happy with the way it worked out. The audio synching module is nicely conceived, but for me the waveform and actual sound file are not synched with each other. My science-based presentation has gaps in the audio for slide transitions, in when I tried using the waveform to define the transition time the sound was off by several seconds. Only by using the audio time indicator numbers was I able to synch the transitions properly. The other problem I had was with one slide that had two rectangular areas containing gradients created by Powerpoint. These looked great in the uploaded Powerpoint slide but the gradients disappeared in the published slidecast. Turns out that these gradients were critical to the point of the slide so this is a serious glitch for me. Any known fixes?