Nick Mitchell here at CD-adapco opened a ticket to ask why his e-mailed comments weren't getting added to issues in JIRA.
Here are the log entries I found:

2014-07-18 06:52:28,976 WARN [jira@cd-adapco.com] QuartzWorker-0 ServiceRunner    Add Comment New This user is not in jira so can not add a comment: Nick Mitchell <nick.mitchell@cd-adapco.com>
2014-07-18 06:52:28,976 ERROR [jira@cd-adapco.com] QuartzWorker-0 ServiceRunner    Add Comment New Add Comment New[10271]: The mail 'FROM' does not match a valid user
 This user is not in JIRA so can not add a comment: Nick Mitchell <nick.mitchell@cd-adapco.com>

Look simple, right? It was.

I found that when we'd created his JIRA account, we'd put a single space at the end of his e-mail address. That was enough to stop the "Add Comment" mail handler from matching the FROM addresses with the e-mail in Nick's account.

Here is what we had entered for his e-mail address:

"nick.mitchell@cd-adapco.com "  <- not a typo, there was really a space

Outbound mail to users from JIRA works fine for Nick.

My guess is that someone didn't think to or choose not to strip trailing whitespace from the e-mail address during user creation and also when matching in the mail handler.

We have our accounts in the internal JIRA user directory, by the way.