Something must have thrown up the flag to run startup repair, perhaps it's the boot animation you're using? Some people on sites like deviantart have been making larger resolution and/or widescreen boot animations. I have not tried any of those because to me that sounds like its pushing it a little. Are you sure the boot animation is in the proper format, size, dimensions, and the correct number of frames?
Good practice there on backing everything up. I assume you have the x64 version of Boot Updater? I would try another boot animation (or a few others) which people have reported as working for them on your version of Windows in the comments, etc.
This has actually happened to me a couple of times, although quite rarely/randomly. I let it run the first couple times it happened, until I became suspicious that all Startup Repair was doing was copying the Vista boot animation over the custom one (for whatever reason). I had reapplied the same animation and rebooted with no problems on the next startup. After that, it'd happened a couple times, but I just hit cancel, and Windows loaded fine, as well as booted up without problems since. I haven't had it happen to me a long time since then, and no problems with system stability.
On my version of Windows I have had Mechanics, Diablo III, and the Umbrella Corporation boot animations from deviantart all working fine.