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Hi Peter,
A beam sampler and a fast photodiode would be very helpful to look at the points A, B, C, and D to narrow down the cause of the problem.
Off the top of my head, I can think of a timing problem between the shutter and the pockels cell or simply a faulty pockels cell. A less obvious problem could be that back-reflection from the pockels cell induces polarization or power instability in the laser that is seen as a power transient. Some lasers have an integrated optical isolator that minimizes back reflection but I don't know if this is the case.
With the photodiode, you will be able to find out if the problem comes from the laser, the shutter, the pockels cell, or perhaps the sample.
I hope this helps a little
--
David Chen
Postdoc
Max Planck Institute for Molecular Cell Biology and Genetics