It looks like bubble trapped between the slide and coverplate.  Are you using
sufficient surfactant?  That can help, but any of the "cap gap" methodologies
lend themselves to this problem.

Rinse your slides very thoroughly in buffer with plenty of surfactant before
loading them on the instrument.
Actually, I don't use any specific surfactant, as long as it is not included in TBS buffer ;) What do you recommend? Maybe just rinsing in buffer would do? I'll give it a try tomorrow, I think.

The bubbles to which I refer to are not coverslipping bubbles,
rather bubbles that were present on the sections during staining that
keep the antibody(ies) and/or the chromogen from making contact with the
tissues. Still, I would think if having that many slides affected, you
probably would have noticed an inordinate amount of bubbles present
between the coverplates and the slides at the time of staining!?!
How can they develop? I did not see any bubbles, because I don't change them between the steps.

Thanks for your replies :)

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