I just moved to another VPS, installed Debian 7 and loaded BOA successfully, then updated because got this message:
apticron report [Wed, 29 Jan 2014 10:20:17 -0500]
apticron has detected that some packages need upgrading on:
The following packages are currently pending an upgrade:
/usr/sbin/apticron: 285: /usr/sbin/apticron: Syntax error: Bad fd number
After update another message:
Time: Wed Jan 29 11:19:14 2014 -0500
The following list of files have FAILED the md5sum comparison test. This means that the file has been changed in some way. This could be a result of an OS update or application upgrade. If the change is unexpected it should be investigated:
/usr/bin/aria_chk: FAILED
/usr/bin/aria_dump_log: FAILED
/usr/bin/aria_ftdump: FAILED
/usr/bin/aria_pack: FAILED
/usr/bin/aria_read_log: FAILED
/usr/bin/innochecksum: FAILED
/usr/bin/my_print_defaults: FAILED
/usr/bin/myisam_ftdump: FAILED
/usr/bin/myisamchk: FAILED
/usr/bin/myisamlog: FAILED
/usr/bin/myisampack: FAILED
/usr/bin/mysql: FAILED
/usr/bin/mysql_config: FAILED
/usr/bin/mysql_install_db: FAILED
/usr/bin/mysql_plugin: FAILED
/usr/bin/mysql_tzinfo_to_sql: FAILED
/usr/bin/mysql_upgrade: FAILED
/usr/bin/mysql_waitpid: FAILED
/usr/bin/mysqladmin: FAILED
/usr/bin/mysqlanalyze: FAILED
/usr/bin/mysqlbinlog: FAILED
/usr/bin/mysqlbug: FAILED
/usr/bin/mysqlcheck: FAILED
/usr/bin/mysqldump: FAILED
/usr/bin/mysqlimport: FAILED
/usr/bin/mysqloptimize: FAILED
/usr/bin/mysqlrepair: FAILED
/usr/bin/mysqlshow: FAILED
/usr/bin/mysqlslap: FAILED
/usr/bin/perror: FAILED
/usr/bin/php-cli: FAILED
/usr/bin/replace: FAILED
/usr/bin/resolve_stack_dump: FAILED
/usr/bin/resolveip: FAILED
/usr/bin/tokuftdump: FAILED
/usr/sbin/mysqld: FAILED
So, is all this normal?

Comments
Hello, I can perhaps give you
Hello,
I can perhaps give you some advice:
1.) You should NEVER post your website domain name or IP address - there is a huge amount of spam, and the spammers probably search boa and drupal sites.
2) You stated that you "updated because you got this message" - my advice is to NEVER update the OS yourself, rather you have to wait until a new BOA release is made, and the BOA release will contain the updates that work with BOA.
Good luck!
Update
Re 2), BOA includes a system-only upgrade mode, which you can run with "barracuda up-stable system", so you don't have to wait for a new boa release. The apticron email also includes these instructions. Agree, never use apt-get etc. to update the system yourself.
As for the md5sum check failures: as the message states, this is expected IF those packages were updated. Otherwise, you should investigate. From what you posted, it seems like these shouldn't have been updated.
What command did you use to update? If you didn't use barracuda, perhaps that explains why some packages like mysql were changed.
So now IP address is gone,
So now IP address is gone, good advice.
However, I never used Debian commands to upgrade system, I used BOA commands, I know that much.
I upgraded the meta-installer to latest version and then executed the command.
That is the reason why I ask if this is normal.
And yes, the command I used was "barracuda up-stable" without system, and it worked.
Right, "barracuda up-stable"
Right, "barracuda up-stable" is fine too of course (I use the system version via cron to exclude updates to barracuda itself).
In this case, if you just ran the up-stable command and you received the md5 comparison mail right after, I think it's safe to assume that the update you ran caused the detected changes, not some malicious activity.
The only thing that seems different from normal: I'm used to first seeing the packages that need upgrading in the apticron email, and then see files related to those same packages in the md5sum check report.
Maybe I deleted mention of
Maybe I deleted mention of the files in the first (apticron) email, when I deleted the IP.
They were 10 files related to Debian, and no these files did not show up in the md5sum report.
What is: "Bad fd number" ?
http://ubuntuforums.org/showt
http://ubuntuforums.org/showthread.php?t=1460684
google search showed this thread, apparently 'Bad fd number' is indeed a syntax error, hopefully it will get corrected in future versions.