One possible cause is that the audio in the right track may have positive peaks that are greater than the negative peaks. This would cause the clips on the bottom half of the right track to be “hidden” from ClipFix because they are at a lesser absolute level than the top of the track. To adjust this there is now a new tool that you can try called “DC offset…” You can get it here: DC offset tool (plug-in) (make sure that you download the “Current Version: dc-offset.ny”)
Use the following settings:
Apply or remove: Remove
Offset removal method: Equal +/- peaks
How much offset to add: doesn’t matter - we’re not adding. Leave at the default 0.0
After applying, try ClicpFix again. Does that work?
After applying ClpiFix you should put the “DC offset” right again.
Apply “DC offset…” again, but change the “Offset removal method” to "Dynamic.
Let me know how you get on.