All users with MIDI clock timing trouble should please check this preference settings:
>File >Preferences... >MIDI/Filter >"Thru SysEx" should be active (checkmarked)!

Some external MIDI devices are constantly sending MIDI clock of their own whether they are set as sync slave or not.
The problem is that MIDI clock will be sent to SX and is "thrued" to the output port again together with the SX MIDI clock signal.
As you can imagine this will end up in a total MIDI clock overkill.

Two possible solutions:
1. Check the preference settings (see above)
2. Check if you can setup your synth not to sent out MIDI clock, the device should just receive it.
This is the safest and recommended mode when working with MIDI clock.

Please always remember that MIDI is a serial protocol.
That means if you have huge amounts of MIDI data to transmit over the same MIDI port used for MIDI clock,
timing fluctuations can occur. When you use MIDI parts with lots of controller data you should try to thin them out.

Furthermore it can help to check if >File >Preferences... >MIDI >"Note On" Priority is set to active.

Also try to avoid the usage of "emulated" MIDI ports. More information about this can be found here:  service.steinberg.de