I know it’s been a long time but I just run in exact same problem, and found out that footage I had to edit (not mine) has an interesting flaw. Any time camera was turned on sound recording would lag for a split second. I only found this out by switching to “Time Ruler Numbers” (CS6) in timeline because it is not visible under frames ruler as lag is not even a second. Never the less, it was enough to prevent sound crossfade audio filters to be placed. Again there were no gap between audio clips in timeline. So I unlinked all audio and video and edited sound by trimming silence in the front of every clip and slowing down all audio clips with “speed/duration” to about 99.9-99.5 % to fill the gaps resulted from trimming. After that crossfade filters worked without any problems. Slowing audio did not affect the resulting footage it looked and sounded perfectly natural.