IOUtils.skip(InputStream, long) and IOUtils.skip(Reader, long) have the worst possible performance as they always use read() on the input instead of using skip(). In many cases, using skip() from a subclass of InputStream is much faster than read(), as the skip() can be implemented via a disk seek.
The IOUtils.skip() methods are also used in the copyLarge() methods that involve a skip.
Case in point: I have observed this performance degradation with Java 7 on Windows 7. A series of consecutive copyLarge() invocations on a large file on disk that involved skips changed my performance from 30 secs as my baseline to 10 minutes after starting to use IOUtils.copyLarge().