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The registry is basically nothing but a file system that holds really small text files. Any software author may read and/or write to it in their installer or their code. It is then up to them to remove anything they add. Several don't, so the registry gets bloated over time.
This wouldn't be as big an issue if it weren't for the fact that when Windows boots it loads the entire registry into memory. That's why people get speed gains the first time they run a "registry cleaner". It shrinks the size of the registry by removing entries that the actual developer wasn't kind enough to clean up.
As for finding the same repairs over and over, it's likely that it's removing keys that are used by one of your apps and that app is constantly having to replace them so it can run.
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