Do you know if it's related to network transfer, or have you narrowed it down to hard drive activity? Maybe you could boot up the Activity Monitor and identify which process is overusing your CPU?
When things get fishy, which I'm very lucky they rarely do, I'll go through my running processes one by one and make sure they are all accounted for. If there's a process you don't recognize, Google its name. If it's legit, chances are it's readily documented out there...
Sorry, just read your second post. If most of your beachballing is happening after iPhoto boots up, consider disabling automatic start-up of iPhoto when plugging in your iPhone, and letting photo sync happen via Wi-Fi? I mean, this shouldn't be necessary, in theory, but if the alternative is beachballing into oblivion, you might be better off letting your media sync unobtrusively via Wi-Fi, in the background...
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