I've got a similar setup, and I also get slight pauses (never a minute
-- more like 6-7 sec.) -- I think it's whenever InDesign needs to access
the second harddrive.
My hunch is that since the primary drive is the SSD, the secondary
regular harddrive is not accessed sufficiently frequently, and so it
spins down. Then, for some operations (in my case, opening the Scripts
panel, since most of my scripts are stored on the second harddrive),
InDesign needs to access it, and it then has to spin up to speed first,
which can take several seconds (a bit like when you put a CD in the
drive, you have to wait a few seconds for the CD to spin up to speed).
Meanwhile, everything grinds to a halt.
Could be I'm completely wrong, and anyway, I don't have a solution to
offer -- just trying to isolate what the cause of the problem might be,
which is one step towards solving it, I guess.
Ariel