There could be many reasons why clear cracks...a few questions (like everyone else).
Is it the clear that cracked? or could it be anything underneath the clear, ie. bodywork, lacquer paint (as mentioned).
Are you finding clear cracking anywhere else especially a top panel like a roof?
What type of clear? Some clears are harder than others and if you have a combination of mil thickness of clear, body work (as clear, some fillers are harder than others and don't allow flex) and primers...If the primer is put on to thick or is a product that can go brittle after a while, cracks can develop.
The sad news is that you may need to take the paint down too and past the substrate to figure out what the problem is. It would be rare that if the clear was applied properly that it would crack without something happening underneath.
As far as waxing goes, I don't believe that would cause clear to crack....if anything it would cause clear to haze off. Some of the older high silicone content waxes seal the clear off to the point where over time would virtually suffocate the clear and cause it to die off.
Hope this helps...a bit anyway.