I used to export my data using option MySQL Admin -> data export/restore -> export to self-contained file, for MyIsam.
But when I switched over to InnoDB and option checked for ‘innodb_file_per_table’ and did my data export using self contained file, and imported it back to other mysql 5.5 machine. It created only one innodb data file for all my database table.
Solution for keeping separate .ibd files for all DB is to check ‘Export to dump project folder’ and then import that folder. Doing this will keep one innodb file per table.