InnoDB takes over an hour to import 600MB file, MyISAM in a few minutes

Did you try the Bulk Data Loading Tips from the InnoDB Performance Tuning Tips (especially the first one):

• When importing data into InnoDB, make sure that MySQL does not have
  autocommit mode enabled because that
  requires a log flush to disk for every
  insert. To disable autocommit during
  your import operation, surround it
  with SET autocommit and COMMIT
  statements:

  SET autocommit=0;
  ... SQL import statements ...
  COMMIT;
  

  If you use the mysqldump option --opt, you get dump files that are
  fast to import into an InnoDB table,
  even without wrapping them with the
  SET autocommit and COMMIT
  statements.

• If you have UNIQUE constraints on secondary keys, you can speed up table
  imports by temporarily turning off the
  uniqueness checks during the import
  session:

  SET unique_checks=0;
  ... SQL import statements ...
  SET unique_checks=1;
  

  For big tables, this saves a lot of disk I/O because InnoDB can use
  its insert buffer to write secondary
  index records in a batch. Be certain
  that the data contains no duplicate
  keys.

• If you have FOREIGN KEY constraints in your tables, you can
  speed up table imports by turning the
  foreign key checks off for the
  duration of the import session:

  SET foreign_key_checks=0;
  ... SQL import statements ...
  SET foreign_key_checks=1;
  

  For big tables, this can save a lot of disk I/O.

IMO, the whole chapter is worth the read.