Dan:

I also use the Skim update feature with latex on the same OS and Skim
as you.  I have not noticed that problem.  However, the macOS can get
bogged down by various processes, especially at startup (e.g. mds). 
Check with top on the command line.  I have a convenient alias:

% alias topcpu
top -o cpu

Then topcpu will show you what process(es) are hogging things.

By the way, check out this way of triggering the latex run:
https://alum.mit.edu/www/toms/atchange.html

Tom

  Thomas D. Schneider, Ph.D.
  Senior Investigator
  National Institutes of Health
  National Cancer Institute
  Center for Cancer Research
  RNA Biology Laboratory
  Biological Information Theory Group
  Frederick, Maryland  21702-1201
  [email protected]
  https://schneider.ncifcrf.gov (current link)
  https://alum.mit.edu/www/toms (permanent link)

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