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I've noticed this behaviour as well. It seems that when the Mantis bug tracker is set as Active on the Modules Administration page, the Search module will only Search through the modules that have an Order number that is higher than Mantis.
For example, if all of your modules are set with an Order of 1 and Mantis is set to 2, the Search function will only search through the Mantis information. However, if you set the Order of Mantis to 2 and News to 3 and all other modules to 1, then search will look through Mantis and News information, but no other module info.
The work around is to Order all modules so that they appear after Mantis. This defeats the purpose of ordering, however, so a permanent fix would be nice.
I will post here if I find out anymore info. Anywone have any ideas in the meantime???