I've got the same problem. Have you made any progress?
I'm still testing, but think I am making progress. Unfortunately, I've learned of no better ways to debug this than trial and error.
Here are some things you can check/try:
1) Ensure you're using the 32 bit ODBC Data Source Administrator to set up the DSN. (From the SysWOW64 folder).
2) Ensure you're using the MySQL ODBC 3.51 Driver.
3) Create/use a System DSN (Not User DSN).
4) Ensure you don't have a conflicting DSN set up in the 64 bit ODBC Data Source Administrator. (May be best to get rid of all 64 bit DSNs at least for setup/ test purposes.)
I'm waiting for a fresh copy of FM to set up a clean install on a test machine. Hopefully it will go smoothly.
System datasource. 64 bit DSN are never used sincefmp is 32 bit (had lots of fun with this in SQL server SSIS also). (run / search box and type ODBC. Select ODBC and not odbc 64)
Linked tables have to have the user and password saved in the dsn itself. Only the server needs to be setup with the DSN used in the external datasource DSN, not each client using linked tables. Script step imports though will need a local DSN as that is all client side.