First make sure you are using the last PDFE version, 1.5 Build 59. Early versions don't fix some of the database errors that produce this kind of error messages.
Now open the database editor, under menu Database>Edit, and if the optimize button is enabled click it to optimized the database. If indeed the optimize operation finish successfully, try now to index the PDFs text content to see what happens.
If problem persist, let's try with a clean database. First backup your actual PDFE database, menu Database>Backup, and now from the database editor selected the database tree root node and delete it, confirming you want to start with a clean database. Now index some PDFs and check if the text content indexer now works fine, and if yes, some bug specific to your old database state is the responsible, but because this error message is generic, and show for any unexpected error, I can't give you a solution without access to the backup copy of your database.