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I run regular anti-malware security scans of my public_html directory through a Wordpress plugin, and after recently installing MyBB (which is working great!) the scan has flagged some files:

global.php
private.php
search.php

Just to confirm, these files are part of MyBB, right? Is there any reason why they may have been flagged?

Thanks!
Yes those are all a part of MyBB. What kind of malware did it flag them as? If you didn't download a fresh copy of MyBB from mybb.com then someone could have tampered with the files, but other than that no those aren't malware.
run file verification tool available at tools & maintenance section of forum admin panel.
do you get above listed files as changed ?
Sometime's antivirus marks legit files as virus, you can consider them as false positive!  other than this, do as .m.  suggested
MyBB 1.x makes heavy use of eval(), likely a false positive but run a file verification check anyway.
File Verification found nothing other than informing me that the /install/ directory is missing (it said to delete it after install?).

So I'm assuming it's a false positive. The forum is brand new other than a few CSS tweaks I have done to the theme.

Safe to say I can whitelist the files on the Anti-Malware scanner?
Yes, they are fine if file verification says they are fine. Feel free to whitelist them.
Just ran another scan and whitelisted the above files, but it had trouble reading this:
/admin/jscripts/codemirror/lib/codemirror.js

and then listed the following as "potential threats"

/announcements.php
/calendar.php
/contact.php
/editpost.php
/forumdisplay.php
/index.php
/managegroup.php
/member.php
/memberlist.php
/misc.php
/modcp.php
/moderation.php
/newreply.php
/newthread.php
/online.php
/polls.php
/portal.php
/printthread.php
/report.php
/reputation.php
/sendthread.php
/showteam.php
/showthread.php
/stats.php
/syndication.php
/usercp.php
/usercp2.php
/warnings.php
/xmlhttp.php
/admin/index.php
/admin/modules/config/settings.php
/admin/modules/forum/management.php
/inc/class_captcha.php
/inc/class_error.php
/inc/class_parser.php
/inc/functions.php
/inc/functions_calendar.php
/inc/functions_forumlist.php
/inc/functions_modcp.php
/inc/functions_online.php
/inc/functions_post.php
/inc/functions_search.php
/inc/functions_user.php
/inc/plugins/hello.php
/jscripts/thread.js
/jscripts/jeditable/jeditable.min.js
if you have original source files of MyBB confirmed through file verification tool then
there should be nothing to worry about your scanner reports (reason is already given in post #5)
(2016-05-17, 04:34 PM).m. Wrote: [ -> ]if you have original source files of MyBB confirmed through file verification tool then
there should be nothing to worry about your scanner reports (reason is already given in post #5)

Just wanted to be sure. Thanks for the clarification.