MySQL 4.0x doesn't support prepared queries, so they're emulated. Emulation means hanging on to the query, and expanding the '?' markers at execute time, substituting appropriately quoted values. However, this isn't a heavyweight operation, particularly not when compared with the overhead of shipping the query over the wire to the server, and waiting for the server to crank on it and return a result.

Assuming (and we have to assume, since we haven't seen code yet, and what we have been shown doesn't verify that results are identical) that query that arrives at the database server process is identical in either case, and assuming that a standalone (non-mod_perl) test doesn't show the the same disparity in timing, then something underneath bind_param is interacting with mod_perl. On a light read of DBD.pm and DBI::MySQL.pm, I can't see what that would be. Curious.