If the 'silence' you added was done via the Captivate Audio dialog then it will be pure silence without any audio data at all and that will just get clipped off by Captivate again. (Weird issue that has plagued Captivate for all time.) You need to make sure the silence at the beginning or end of a clip is NOT pure. So the best thing to do is copy some 'dirty silence' from some pause in the middle of the same clip and paste that into the beginning or end of the clip. Since this silence isn't pure and has at least some low-level audio data, Captivate will leave it alone. That might help part of your issue.
Another thing is to make sure there is at least one blank slide with no objects or audio right at the beginning of your project. NEVER start a project with a slide that needs to have audio playing immediately. Captivate seems to benefit from having a full slide of a second or so to set up BEFORE playing content.