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Your hard drive is having trouble. It's probably set to spin down way too frequently and so it spins up when it's got to read a program from the disk (load it the first time). This takes a good long time. After that, the program's in memory so it pops right up. I'd check your energy saver settings and see when the hard drive is set to spin down. Set it to "never", reboot and see if you still have the same problem.
Anyway, I'm confident it has to do with reading the program off the hard disk and into memory. I gar-on-tee it!
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