I have experienced the following problem after making some audio-cd copies : several tracks on the disk cannot be accessed directly on my audio cd-player although when the cd is played continuously it works fine. If I am using for playing the cd my cd-rom or my writer everything is OK and I can directly access all the tracks.
This happen sometimes, when the writer starts loosing the ability to find the correct positions for writing and the actual gaps are not 100% on the correct positions. Usually this happens to Yamaha writers sooner or later. So try to lower the writing speed and try different CD-R media. But it is also possible that a writer is not able to write very short gaps, so make sure that in the CUE sheet each gap is bigger than at least 100 sectors (1 1/3 second).