Hi Raphie,
Do you have Wavelab and Cubase open at the same time?

Have you tried this with just the MADI card in the system?

Have you double checked your Alpha Link settings and routing options?
They are complicated and it can be easy to have something set wrong.

Here is the list I use that is from SSL's  knowledge base for settings up an ALphalink to a RME MADI card.
I have not done any mixed card setups other than 2 MADI cards so i do not know how have a non MADI in the setup could effect things.
It seems from your posts that the clock is setup right. I would double check your Alphalink settings and test this with out the Raydat in the system.

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Both the MADI-SX and the MADI-AX are covered, you can pick what you need if you write to a customer. Obviously you would pick the bits that relate to the I/O type the client wants to use.

Alpha-Link MADI-AX connected to MADI DAW:

A) Routing ANA In to MADI Out (for recording)

1) Press the OUTPUT button, repeatedly if necessary, until the MADI Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the ANA Input LED *only* is lit (the ADAT input LED should be off).
3) Release the buttons. ANA In is now routed to MADI Out.

B) Routing MADI In to ANA Out (for playback)

1) Press the OUTPUT button, repeatedly if necessary, until the ANA Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the MADI Input LED is lit.
3) Release the buttons. MADI In is now routed to ANA Out.

C) Making sure MADI In is not going to ADAT Out.

1) Press the OUTPUT button, repeatedly if necessary, until the ADAT Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until all the Input LEDs are off.
3) Release the buttons. You can now be sure that MADI channels 1-24 are not going to the ADAT Outputs instead of the ANA Outputs.

D) Routing ADAT In to MADI Out (for recording)

1) Press the OUTPUT button, repeatedly if necessary, until the MADI Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the ADAT Input LED *only* is lit (the ANA input LED should be off).
3) Release the buttons. ADAT In is now routed to MADI Out.

E) Routing MADI In to ADAT Out (for playback)

1) Press the OUTPUT button, repeatedly if necessary, until the ADAT Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the MADI Input LED is lit.
3) Release the buttons. MADI In is now routed to ANA Out.

F) Routing ANA In and ADAT In to MADI Out (for recording)

1) Press the OUTPUT button, repeatedly if necessary, until the MADI Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the ANA Input LED and the ADAT input LED are both lit.
3) Release the buttons. ANA In and ADAT In are now routed to MADI Out.

Alpha-Link MADI-SX connected to MADI DAW:

A) Routing ANA In to MADI Out (for recording)

1) Press the OUTPUT button, repeatedly if necessary, until the MADI Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the ANA Input LED *only* is lit (the AES input LED should be off).
3) Release the buttons. ANA In is now routed to MADI Out.

B) Routing MADI In to ANA Out (for playback)

1) Press the OUTPUT button, repeatedly if necessary, until the ANA Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the MADI Input LED is lit.
3) Release the buttons. MADI In is now routed to ANA Out.

C) Making sure MADI In is not going to AES Out.

1) Press the OUTPUT button, repeatedly if necessary, until the AES Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until all the Input LEDs are off.
3) Release the buttons. You can now be sure that MADI channels 1-24 are not going to the AES Outputs instead of the ANA Outputs.

D) Routing AES In to MADI Out (for recording)

1) Press the OUTPUT button, repeatedly if necessary, until the MADI Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the AES Input LED *only* is lit (the ANA input LED should be off).
3) Release the buttons. AES In is now routed to MADI Out.

E) Routing MADI In to AES Out (for playback)

1) Press the OUTPUT button, repeatedly if necessary, until the AES Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the MADI Input LED is lit.
3) Release the buttons. MADI In is now routed to AES Out.

F) Routing ANA In and AES In to MADI Out (for recording)

1) Press the OUTPUT button, repeatedly if necessary, until the MADI Output LED is lit. Then hold down the OUTPUT button.
2) While holding down the OUTPUT button, press the INPUT button, repeatedly if necessary, until the ANA Input LED and the AES input LED are both lit.
3) Release the buttons. ANA In and AES In are now routed to MADI Out.

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Thanks Chris