Hi, did you get your problem solved? I have the same problem. Thanks,
Is your server on a Linux or Windows box?
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From the administrative tool, open the 32 and 64 bit odbc Data sources and create identical UserDSN to your mysql in each one, and it should work.
You have to make sure you have both the 32 and 64 bit odbc drivers and then with creating identical sources with them the 64 bit server and the 32 bit client can both see mysql.
I installed both MySQL 5.3.4 32bit and 64bit driver. I am able to create an ODBC connection file from ArcCatalog, and I am able to see the table in MySQL. Nevertheless, I cannot use the ODBC connection file to register database in the datastore in ArcGIS server 10.2.2. ArcGIS server gave me "General function failure".
That was the same exact problem I was having. It is because when you create the connection from catalog it is only creating the 32 bit connection and server does not know what to do with it. If you create your connections from windows first by creating the same connection for 32 and 64 bit then when you select it from catalog you should be able to register it in the datastore
These are the steps that I have done on a Windows 2008 R2 64 bit server. Both 32 and 64 bit MySQL ODBC drivers have been installed.
1. use the 64 bit odbcad32.exe in %systemdrive%\Windows\System32 folder to create ODBC data source under User DSN.
2. use ArcCatalog to add OLE DB connection and selected the ODBC source created in step 1. ArcCatalog has no problem creating the odc connection file and no problem connecting to MySQL DB. However, ArcGIS server complained "general function failure" when importing this odc connection file in step 1 to register in datastore.
3. use the 32 bit odbcad32.exe in %systemdrive%\Windows\SysWoW64 folder to create ODBC data source under User DSN.
4. use ArcCatalog to add OLE DB connection and selected the ODBC source created in step 3. ArcCatalog has no problem creating the odc connection file and no problem connecting to MySQL DB. However, ArcGIS server complained "general function failure" when importing this odc connection file in step 3 to register in datastore.
Exact same issue. Did you ever have any luck?