Trying to recover/import/transfer database from MySQL data dir
I managed to find a workaround for this but I am not very happy about it.
I installed my previuos setup which was EasyPHP and copied my old MySQL *data* dir into the EasyPHP *MySQL* data directory.

This time around the database was able to read the .ibd / .frm files correctly.(even though these files did not change at all)

I then used phpMyAdmin to export the database(this time around all tables/data was stored in the sql file)

I then disabled EasyPHP enviroment and started up my new enviroment and used phpMyAdmin->import with the new sql file which loaded the data correctly.

Overall I think its pretty poor that MySQL cant simply output some type of notice stating that the .ini enviroment variables are not set corresponding to the .ibd / .frm files rather than just output incorrect information and leave the user in the dark with all sorts of angles to think about. After googling around it seems many people seem to believe that their data is corrupt when that's really not the case.