Starting with 12.0.1, the 32-bit MobiLink server is no longer supported on 64-bit operating systems.

This means that if you accidentally CONTINUE to use the 32-bit MobiLink server and client on the same machine after upgrading to 12.0.1, you will suddenly get a "Protocol version mismatch" as shown below.

That's because the old version 12.0.0 32-bit version of mlsrv12.exe is not removed by the 12.0.1 installation even though a 12.0.1 copy is not installed. However, the 32-bit version of dbmlsync.exe is installed. That means when you run the same sync setup that worked before, it starts failing with the oh-so-meaningful "Protocol version mismatch".

As Volker pointed out in a comment, this is not a bug... but it sure as heck is confusing :)

I. 2011-03-07 09:24:00. SQL Anywhere MobiLink Server Version 12.0.0.2601
...
I. 2011-03-07 09:30:07.  System event on shared administrative connection:
                        SELECT property_set_name, property_name, property_value FROM ml_property WHERE component_name = ? ORDER BY property_set_name 
I. 2011-03-07 09:30:07.  Translated SQL:
                        SELECT property_set_name, property_name, property_value FROM ml_property WHERE component_name = ? ORDER BY property_set_name 
E. 2011-03-07 09:30:31.  (,) [-10004] Protocol version mismatch -- expecting 49 but received 65
I. 2011-03-07 09:30:31.  (,) failed reading command with id:1 and handle:1

I. 2011-03-07 09:30:31.  (,) Synchronization failed

I. 2011-03-07 09:29:40. SQL Anywhere MobiLink Client Version 12.0.1.3152
...
I. 2011-03-07 09:30:31. Waiting for MobiLink to apply upload
E. 2011-03-07 09:30:31. Error code from MobiLink server: -10244
E. 2011-03-07 09:30:31. Server error: The MobiLink server has encountered an error and the synchronization has been aborted
E. 2011-03-07 09:30:31. Data read failed.  Requested 2 bytes but got 0 bytes.
E. 2011-03-07 09:30:31. Unable to read 0 bytes.
I. 2011-03-07 09:30:31. End synchronizing subscription(s) 'clifit'
I. 2011-03-07 09:30:31. Disconnecting from MobiLink server