Hi dspunky
The whole trypophobia concept is something I've become intrigued with but - until now - had not looked into it. I've still only scanned parts of information on what I might call an educated guess.
What I've looked at so far is based on my (limited) understanding that the brain processes images in certain ways. This is referred to as visual perception. In some cases there are reported times where "visual discomfort" arises - but so far I've only read about things like reading lines in a book. But there is some research out their that looks at "spatial awareness" and "global pattern percept".
From what I read there is little knowledge beyond the suggestions that some people suffer discomfort when viewing certain things. This may be related to what you say happens to you - and may also be relevant to trypophobia in general.
Basically - the brain sees things it is not happy with - or can't compute or reconcile in it's normal way - hence it becomes a discomfort. There is a similar trait in autistic people who cannot abide abstract or irregular patterns.
I'm not suggesting any of this is all related - but I do consider that the discomfort and unpleasantness associated with the cracks - and those with pattern-phobia - may well find that the issue lies in the capacity of, or the manner in which, the brain interprets visual information.
This may not help you towards a "cure" for the issue - but understanding possible explanations can sometimes alleviate the worry about what it might be. I'm not saying I'm right - but I will guarantee - there's a reason for it.
Some pages I read:
http://clinicaltrials.gov/ct2/show/record/NCT00402155http://www.perceptionweb.com/perception/fulltext/p27/p270021.pdf [PDF]
Search terms that may be of use:
"global pattern percept"
"visual pattern discomfort"
But it's all a bit technobabbly!
If anyone finds any other links of interest please post them.
Hope this helps.