Hi John,
Sorry, that sucks. The way it works is big3d startup scripts first look to see if there is a newer version in /shared/bin/. Newer versions are installed by EM/GTM/etc. If one doesn't exist, it will use the default version of the install in /usr/sbin/
Historically, it could be starting due to various issues like signatures/permissions, etc. You can use the solution below to debug and see if there's any reason logged.
sol10999: Error Message: Re-starting big3d
http://support.f5.com/kb/en-us/solutions/public/10000/900/sol10999.html?sr=18711325
Or you could open a case with support to help find out what the exact issue is or if this is a known issue with that particular combination of Mgmt Pack + BIGIP version. I know Dev has been working on this issue so opening a case on this and having it attached to the appropriate bug ID will help draw attention to the issue.
if really needed to stop big3d from restarting right now, you can just remove the "newer one" and restart big3d (like below) so it uses the default one.
[root@ltm1:Active] config /usr/sbin/big3d -v
/usr/sbin/big3d version big3d Version 10.2.3.112.0 for linux
[root@ltm1:Active] config
[root@ltm1:Active] config ls -lart /shared/bin/big3d
-rwxr-xr-x 1 root root 3869783 Dec 15 06:05 /shared/bin/big3d
[root@ltm1:Active] config /shared/bin/big3d -v
/shared/bin/big3d version big3d Version 10.4.0.12.0 for linux
[root@ltm1:Active] config
[root@ltm1:Active] config
[root@ltm1:Active] config ps -ef | egrep -i big3d | egrep -v grep
root 3736 3553 0 2011 ? S 0:00 runsv big3d
root 3790 3736 0 2011 ? S 3:17 /shared/bin/big3d
[root@ltm1:Active] config rm /shared/bin/big3d
rm: remove regular file `/shared/bin/big3d'? y
[root@ltm1:Active] config ps -ef | egrep -i big3d | egrep -v grep
root 3736 3553 0 2011 ? S 0:00 runsv big3d
root 3790 3736 0 2011 ? S 3:17 /shared/bin/big3d
[root@ltm1:Active] config bigstart restart big3d
[root@ltm1:Active] config ps -ef | egrep -i big3d | egrep -v grep
root 3736 3553 0 2011 ? S 0:00 runsv big3d
root 16996 3736 32 05:40 ? D 0:00 /usr/sbin/big3d
-Alex