Customs searches of computer data brought across the border has been going on way, way before 911.
Be glad they didn't confiscate the data and/or copy it. They easily could have, if they'd wanted to.
FedEx is certainly a good work-around, but not fool-proof when it to Customs. A better way is to upload the data via a secure VPN prior to departure.
TrueCrypt is a good compremise of security and privacy, if one believes that Customs will only do a cursory look at one's computer - ie. ask to turn it on, do a browse of the default My Documents / My Pictures folders.
If they choose to do a more through search, they may stumble upon the TrueCrypt software (or signs of it, such as a password screen) - just the mere existance of such encryption may be enough to arise suspicions - and once Customs get going, as the OP found out, they will spend a seemingly endless amount of time examining everything.
Ron
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