block ios reload shouldn't have any impact on launching cfg usb loader itself (only impacts how games are launched after cfg usb loader is started).
What cIOSs do you have installed? Specifically what cIOS you have installed to slot 249? If you used ModMii to mod your wii you should have a d2x cIOS with base 56, which should be fine, but you'll need v6 or higher of d2x in order for block IOS reload to work properly (v6 was released around June 2011). If you need to update your cIOSs, just use ModMii to update your softmods (see my signature).
I know skyward sword requires you watch the motion + video before being able to play the game, have you watched this video before (either for this game or another game)? If not, change the alt-dol to disc, watch the video, then change the alt-dol back to it's original setting.
The fact that you are getting freezes while in configurable before launching a game tells me your problem is most likely either an outdated cIOS or an issue with your hard drive itself. The weird thing is that you claim the issue started after enabling block IOS reload... it's possible that's a coincidence, but I hate coincidences. Anyways, I suggest you ensure any sleep timers your HDD might have are disabled. Some HDDs come with software on them that you can install and use to disable the sleep timer (ie. Seagate dashboard or WD Smartware), but some do not. If no software came with your HDD, google for Ashampoo HDD Control and install the free version, it will allow you to disable sleep timers on a number of HDDs that don't come with software to help you do it.
