Flashing Question Mark on Folder Icon on Startup: Not Yet Fatal

I running into a potential problem with my White, 13" MacBook. I'm running 10.5.6 (upgraded from 10.4).
I recently bought a new, larger capacity hard drive. I used the Applications "SuperDuper" to clone my existing drive onto the new drive. My computer runs (as far as I can tell) the same as it always did. However, whenever I startup the computer, it briefly flashes the dreaded "giant folder with a blinking question mark". However, this is quickly replaced with the Apple Logo, and the computer boots normally.
I have repaired permissions, and verified the disk using disk utility. The disk verified with a message along the lines of "The disk appears to be ok".
While my computer's working now, I'm concerned there might be a deeper problem, and I'd like to catch it before it becomes critical. Also, if this is something standard that happens when you replace a hard drive with a new one, I'd like to know that as well so I can stop worrying.
If your answer is "put your old drive back in", pretend I did that and am still seeing the problem. What now?
Possible data point, I opened the console and saw the following two lines right before the "got boot device" line
4/29/09 5:00:07 PM kernel Waiting on <dict ID="0"><key>IOProviderClass</key><string ID="1">IOResources</string><key>IOResourceMatch</key><string ID="2">boot-uuid-media</string></dict>
4/29/09 5:00:07 PM kernel AppleYukon2: 532111ab,00000000 sk98osx_dnet - CheckDictionaryEntry failed, expected vs. dictionary
Thanks in advance for your help.

Open Startup Disk preferences, select your startup volume from icon list, click on the Restart button.

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