This has to be something to do with file creation dates. The clock on either your Touch or your computer has the wrong date. Your Touch should automatically get the right date via WiFi (or 3G if you have it), so I think it is likely your PC at fault but it could be the Touch. It does not really matter that they are wrong, what matters is that they are different.
What I think is happening is that all your side-loaded ebooks have a date stamp created by your PC and these are in the future (with respect to the clock on your Touch) - so every time a new file is created the re-indexing kicks in and the index program thinks all your files are new (created after the index).
If you connect your Kindle to a PC, the "data modified" for each file should be displayed if you are in the "details" view. Compare them to the actual date and time and also look for files created by the Kindle, e.g. .mbp files and see if they show much different dates.
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