Images from SD card not showing on OS X

I am in an issue that is a bit of a pain for my workflow.
I explain first what I do so I will avoid questions about the origin of the cause (if I can).
I am using CHDK (a firmware hack for P&S Canon cameras) to shoot time lapses over several days.
So I end up with thousands of pictures on the SD card.
The SD card is Fat32 for CHDK bootable in camera reason.
The images are in separate DCIM folders on the SD card. During the course of the time lapse the image naming counter can reach 9999 and reset to 0001, not a big deal as the camera changes folders automatically in that case, and every day anyway (1800 images a day, approx)
When I put the SD card on my Mac Book Pro 2012 or my Mac Pro, both running 10.8.2, not all the images show up in the Finder.
In the present case out of 5000+ images 495 were missing, and I cannot find a rule for what shows up or not. Some images in all folders are missing.
When I try to import from Aperture, miracle I can see them all. But at the end of the import I get an alert that 495 images could not be imported.
And, finally, when I check the SD card on Windows 7 I can see them all, import them all, no problem.
Well it is a bit of a pain to have to go through Windows for that.
So what's going on? Somehow Mac OS X has some problems with large number of files on Fat32? or what?
I know this is quite specific and unusual bug but I post here just in case it happened to anyone before and that person reads the thread :-D

Forgot to add I tried on a Mini 10.7.5 and get same problem...
So not Mountain Lion specific.

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Occam's Razor nearly always applies when troubleshooting technology issues!
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