Stafano thanks for your reply
I have inherited an sme 8 server at a client on which a special application was loaded for 50+ users.
so far, I can't see any problem

The problem with the application is that i have to keep "Manually" Starting it in " etc/rc.d/rc7.d " every time the sme server reboots.
why? I mean.. any application having a startup script can be a SME's service..
config set myapplicationname service status enabled
in this way SME's knows how to/if start the service at startup
cd /etc/rc.d/init.d
ln -s myinitscript myapplicationname
this should be not necessary: we are creating a symlink of the original startup script with a new name (the point is that myapplicationname must be identical to the service name above)
cd /etc/rc7.d
ln -s /etc/rc.d/init.d/e-smith-service SXXmyapplicationname
we create a symlink to e-smith-service startup script with a name where:
S tells SME to start
XX are numbers.. you can decide when to start the service (you should not start something that need the network before the network itself is up and running)
myapplicationname.. you already know

To make matters worse the application only seems to " start " when i manually start it after a certain time period of a sme reboot.
any ideas? 
yes.. you should start debuggin it..
alternatively at the approach above mentioned, google can help you
"crontab n minutes after reboot" -> google -> first result
I personally would investigate and keep everything as clean as possible
HTH
P.S. telling us the application name could help us to help you