Steve,
Do you know how to use phpMyAdmin? Did you use the Database backup tool to make a full backup before uploading your new data? Did you work on a test version of your website before doing so on your live site?
If you do a full export and PM me with a link, I'll look at your data. You are using 1.2.5.4? Not some other version? Some of the other versions have "issues" ...
One thing to note, the ADMIN search and STORE FRONT search are not the exact same. There are differences, but I am not the right person to numerate them.
It may simply be a parameter.
Does your categories tree in the Admin work correctly? You don't have duplicate item numbers? Do you have any linked products?
-cj
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