If you think that it doesn’t matter how you installed it and on what OS and you think that asterisk 1.6.2.9 is the latest and you installed it on Ubuntu with a squeeze .deb and you think that the problem is the app, then I suggest you get in touch with whoever packaged that version, or maybe the linux fairies, it really DOES matter, all linii are not the same, and FreeBSD is not even linux ;), believe me!!
FYI the latest version of Asterisk 1.6 is as of today 2012-08-15
2012-04-23 asterisk-1.6.2.24.tar.gz
as to 1.6.2.9, then
2010-06-18 asterisk-1.6.2.9.tar.gz
FYI
2010-07-23 README-1.6.2.10
2010-06-29 README-1.6.2.10-rc1
2010-07-14 README-1.6.2.10-rc2
2010-08-10 README-1.6.2.11
2010-07-23 README-1.6.2.11-rc1
2010-07-27 README-1.6.2.11-rc2
2010-09-15 README-1.6.2.12
2010-08-24 README-1.6.2.12-rc1
2010-09-15 README-1.6.2.13
2010-11-11 README-1.6.2.14
2010-09-21 README-1.6.2.14-rc1
2010-12-08 README-1.6.2.15
2010-11-23 README-1.6.2.15-rc1
2011-01-18 README-1.6.2.15.1
2011-01-14 README-1.6.2.16
2010-12-15 README-1.6.2.16-rc1
2011-01-18 README-1.6.2.16.1
2011-02-21 README-1.6.2.16.2
2011-02-28 README-1.6.2.17
2011-01-18 README-1.6.2.17-rc1
2011-01-26 README-1.6.2.17-rc2
2011-02-16 README-1.6.2.17-rc3
2011-03-16 README-1.6.2.17.1
2011-03-17 README-1.6.2.17.2
2011-04-21 README-1.6.2.17.3
2011-04-26 README-1.6.2.18
2011-02-28 README-1.6.2.18-rc1
2011-06-23 README-1.6.2.18.1
2011-06-28 README-1.6.2.18.2
2011-06-29 README-1.6.2.19
2011-06-24 README-1.6.2.19-rc1
2011-08-05 README-1.6.2.20
2011-12-08 README-1.6.2.21
2011-12-19 README-1.6.2.22
2012-03-15 README-1.6.2.23
2012-04-23 README-1.6.2.24
(sorry, I am being an ass here, and having too much fun, 2012-04-23 README-1.6.2.24 will cover everything)
Even non mindreaders won’t call two years ago “latest”, especially as that was before the Skype channel driver was released
So you will need Asterisk and asterisk-addons in 1.6 (1.8 and above preclude that addon reqirement)
the digium site is quite helpful there, so go there, download it, read the rules and do it.
http://www1.digium.com/en/products/asterisk/downloads
In case you are tempted to get FreePBX from a similarly outdated source, I suggest you get the “real” latest FreePBX with
svn http://www.freepbx.org/v2/svn/freepbx/branches/2.10/
Your trouble is if you install it yourself you have to fix it yourself, few will have the patience to do it for you. Not that I don’t applaud you for going that way, I am also an autodidact, unfortunately that will leave you swinginging in the wind until you pull yourself up by your bootstraps (wow, there is a rather incongruent mixed metaphor!), few will help you there, the rewards are great though.
Gently, I suggest you start with a proven and accepted distro first, (to my knowledge as yet you will be limited to Centos for some strange legacy reason) when you get to wear big boy boots, then absoultely, install on Debian, Ubuntu, FreeBSD or even WinBlows, it is all open source and depends pretty well on other open source projectsm good luck with zend on FreeBSD or CPM though if you want commercial modules.
When you have a relatively current and otherwise working sysytem, then is maybe the time to whine about your Digium code, but as previously stated, the Skype code is presumably from Digium and you presumably paid for it, does it not make sense to bug them about their bugs first ?
To my knowledge there is nothing in FreePBX that has any touch on Skype trunking apart from assuming you got it working first.