When upgrading a router from 2.9.xx (either .38 or .50), using the single-package for mipsle, not all appropriate packages were transferred. Missing and important to us were advanced-tools and security. We had to download the zip file of all packages and individually upload the missing ones. PITA!
oh, yes! is it possible to install additional packages with full-package?
I upgraded router from 2.9 to 3.0 with mipsle,
advanced-tools and security package are installed together with all-in-one package.
Probably these packages were not installed before you go with upgrade.
Chupaka,
it is possible to upload other packages together with all-in-one package, additional packages like dude User-Manager will be installed.
sergejs, but if I have only all-in-one package, can I install packages, that are not installed yet? When I upgrade, only existing packages upgrade
Yes you can ad as many package that you like at the same time 
but how? upload package second time and reboot again?
Only add as many new packages as you like to add at the same time as you install the main package.
omg… please read once again:
well, i upgraded my 3.0 to 3.1…
first, uploaded routeros-x86-3.1.npk. rebooted. version 3.0, and routeros-x86-3.1.npk disappeared from router… well, uploaded routeros-x86-3.1.npk again… rebooted… yes, 3.1! but!.. only system package, others have gone =) uploaded third time, rebooted - yes, all packages installed =)
It is not clear for me,
well, i upgraded my 3.0 to 3.1…
first, uploaded routeros-x86-3.1.npk. rebooted. version 3.0
Could you give us step by step description, how do you get only system package installed ?
As usual, I uploaded 3.1 all-in-one package to router (ros v3.0) and rebooted. package disappeared from FTP, but nothing else changed: all versions remain 3.0. after second upload and reboot, I saw only 3.1 system package =) and in Log, there were 4 empty messages
what about log file?
Do you able to reproduce this issue on other router ?
I have upgraded multiple routers from 3.0 with 3.1 with all-in-one package without any issues.
unfortunately, at the moment I have only one router to play with v3, so I am not able even try to reproduse this =(