H.264 video typically contains a high keyframe interval. When recording is started between twokey frames, Flash Media Server drops all video intermediate frames (i-frames) until the first keyframe is received. This issue only affects video i-frames; audio i-frames are recorded as received.
This behavior is expected for Flash Media Server. You can cause the server to start recording video i-frames sooner by shortening the keyframe interval. Or, you can push the first keyframe to the server as soon as possible.