I think you have it wrong...

clamd.conf would only be read by the clam daemon...

freshclam.conf on the other hand is read by freshclam when it does its
update (or how to configure that daemon)...

I run my freshclam via a cronjob, so I don't know exactly how one
would configure in daemon mode...

However, with that said you want to make sure you have the following
line commented so its not trying to notify clamd (which is what it
sounds like its doing):

# Send the RELOAD command to clamd.
# Default: no
#NotifyClamd /path/to/clamd.conf

The "Checks" setting is if you are running in daemon mode, for how
often freshclam would check for updates.
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