Yes, I too was having problems noting that mine were related to drives mounting / not mounting properly, weird behaviour with multiple applications, etc....AppleCare suggested I do a fresh instal which I did not want to do but eventually succumbed to and all was well...
Theoretically there shouldn't be a difference huh. I am thinking because iPhoto and GarageBand are preinstalled with it and when you start your mac for the first time it brings up the account set up that they have a modified install version for their os x so it includes iPhoto and GB in the installation all in one shot. Perhaps their version slightly modifies stuff for the specific computer it is going onto vs buying the generic ML that fits their whole range.
Apart from that I am stumped as to why a fresh install myself will make two of my apps work but a fresh preinstall this month by Apple screws stuff around. Could be Corel and Adobe's fault too but I was using Mountain Lion since release on my previous mac with both of those applications, no issues whatsoever.
Right now I don't really require Corel Painter and Illustrator I have bandaided by removing a culprit file I am 99% sure I don't require but once I get an external drive I will probably clean install ML.
Thanks for your input guys