Nintendo finds it necesarry to make their images a full 4.5 (4.1) GB even though the games may be much, much smaller (Wii Chess lol).
They do this by putting alot of garbage data in the ISOS to take up place, so it becomes exactly 4.5 (4.1) GB.
Scrubbed images are simply those same images, except with the garbage data replaced by easily compressed data.
So yeah, scrubbed games basically means the garbage that came with the game was replaced, the game itself is not changed at all. And thus, there SHOULD not be ANY difference between a scrubbed or an original garbage game being played.
I and everyone i know have yet to experience any, so yeah, I highly doubt any problems you have with a scrubbed game are BECAUSE they were scrubbed, keep in mind the compatibility of the loader is not perfect and neither is the loader itself.