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Have you ever tried to install MySQL ODBC 5.3 Connector without Tableau?
Maybe this behaviour be part of MySQL ODBC Connector.
Yes, we have run these connectors concurrently for a while and have never had this issue, but I will test this in isolation to make sure this is still true.
I just thought that maybe version 5.3 can be uninstalling version 5.1
You're absolutely right.
With both 32-bit and 64-bit 5.1 installed, installing/updating/repairing any 5.3 installation uninstalls all 5.1 installations.
Thankfully, the connectors come as MSIs so I can get the machines to install them via Group Policy whenever they are missing.