When it doesn't boot normally I'd assume you've added or removed a game (Wii, GC or EmuNAND), since that'll trigger the loader to automatically rebuild the cache files.
Based on the USB HDD activity LED it looks like files are being searched for, but the seek/access time is abnormally long
- If enabled, where are your EmuNAND files located?
- Does your theme load any custom music?
- If you disable caching (settings > features > cache titles) is booting always slow?
- Have you tried resetting the loader to it's default settings?
- Have you tried setting the loaders IOS to 251 and then restarting the loader?
Are they different brands or models and do they all contain the exact same content?