So I presume latrace is the only one you can upgrade because its for free; have you tried uninstalling latrace first. It can always be installed to the latest version later on but first uninstall it to see if your icon issues still trouble you...

~ # apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be upgraded:
chaos-control flowplayer latrace
meegotouchhome-nokia-settings squareit
5 upgraded, 0 newly installed, 0 to remove and0 not upgraded.
Need to get 2,815kB of archives.
After this operation, 640kB of additional diskspace will be used.
Y
WARNING: The following packages cannot be authenticated!
latrace
Install these packages without verification [y/ Y
Get:1 [715kB]
0% [1 chaos-control 0B] [Connecting to harmatt../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: PendingRegistration
../../../lib/SignOn/authsessionimpl.cpp 178 initInterface
../../../lib/SignOn/authsessionimpl.cpp 280 process sending to queue
0% [1 chaos-control 0B] [Connecting to harmatt../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: Ready
../../../lib/SignOn/dbusoperationqueuehandler.cpp 131 execQueuedOperations Executing cached oparation: SIGNATURE: process(SessionData,QString)
../../../lib/SignOn/dbusoperationqueuehandler.cpp 138 execQueuedOperations
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
0% [1 chaos-control 0B] [Connecting to harmatt../../../lib/SignOn/authsessionimpl.cpp 172 checkConnection
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
Get:2 http://harmattan-dev.nokia.com harmattan/sdk/free latrace 0.5.11-2~git2849dc0+0m6 [161kB]
1% [1 chaos-control 0B] [2 latrace 29.5kB/161kQNetworkReplyImpl::_q_startOperation was calledmore than once
2% [1 chaos-control 0B] [2 latrace 68.5kB/161kFatal error: Server sent invalid DownloadUrl
Err
Sub-process returned an error code
Get:3 [1,150kB]
2% [3 flowplayer 0B] [2 latrace 82.4kB/161kB 5../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: PendingRegistration
../../../lib/SignOn/authsessionimpl.cpp 178 initInterface
../../../lib/SignOn/authsessionimpl.cpp 280 process sending to queue
../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: Ready
../../../lib/SignOn/dbusoperationqueuehandler.cpp 131 execQueuedOperations Executing cached oparation: SIGNATURE: process(SessionData,QString)
../../../lib/SignOn/dbusoperationqueuehandler.cpp 138 execQueuedOperations
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
3% [3 flowplayer 0B] [2 latrace 88.7kB/161kB 5../../../lib/SignOn/authsessionimpl.cpp 172 checkConnection
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
4% [3 flowplayer 0B] [2 latrace 123kB/161kB 76QNetworkReplyImpl::_q_startOperation was calledmore than once
5% [3 flowplayer 0B] 7,171B/s 6min 10sFatal error: Server sent invalid DownloadUrl
Err
Sub-process returned an error code
Get:4 [615kB]
5% [4 squareit 0B] 7,171B/s 6min 10s../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: PendingRegistration
../../../lib/SignOn/authsessionimpl.cpp 178 initInterface
../../../lib/SignOn/authsessionimpl.cpp 280 process sending to queue
../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: Ready
../../../lib/SignOn/dbusoperationqueuehandler.cpp 131 execQueuedOperations Executing cached oparation: SIGNATURE: process(SessionData,QString)
../../../lib/SignOn/dbusoperationqueuehandler.cpp 138 execQueuedOperations
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
5% [4 squareit 0B] 7,171B/s 6min 10s../../../lib/SignOn/authsessionimpl.cpp 172 checkConnection
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
5% [4 squareit 0B]QNetworkReplyImpl::_q_startOperation was called more than once
5% [4 squareit 0B]Fatal error: Server sent invalid DownloadUrl
Err
Sub-process returned an error code
Get:5 [174kB]
5% [5 meegotouchhome-nokia-settings 0B]../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: PendingRegistration
../../../lib/SignOn/authsessionimpl.cpp 178 initInterface
../../../lib/SignOn/authsessionimpl.cpp 280 process sending to queue
../../../lib/SignOn/identityimpl.cpp 105 updateState Updating state: Ready
../../../lib/SignOn/dbusoperationqueuehandler.cpp 131 execQueuedOperations Executing cached oparation: SIGNATURE: process(SessionData,QString)
../../../lib/SignOn/dbusoperationqueuehandler.cpp 138 execQueuedOperations
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
5% [5 meegotouchhome-nokia-settings 0B]../../../lib/SignOn/authsessionimpl.cpp 172 checkConnection
../../../lib/SignOn/authsessionimpl.cpp 276 process sending to daemon
5% [5 meegotouchhome-nokia-settings 0B]QNetworkReplyImpl::_q_startOperation was called more than once
5% [5 meegotouchhome-nokia-settings 0B]Fatal error: Server sent invalid DownloadUrl
Err
Sub-process returned an error code
Fetched 161kB in 1min 7s (2,393B/s)
Failed to fetch exec:////usr/bin/osa --get 'chaos-control' Sub-process returned an error code
Failed to fetch exec:////usr/bin/osa --get 'flowplayer' Sub-process returned an error code
Failed to fetch exec:////usr/bin/osa --get 'squareit' Sub-process returned an error code
Failed to fetch exec:////usr/bin/osa --get 'meegotouchhome-nokia-settings' Sub-process returned an error code
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

Problem is I dont know what is this latrace... it does not appear in the applications list, not there is an icon in desktop. And to be honest, I dont know which application is this!

Does it have to do with this:
http://harmattan-dev.nokia.com/docs/...g_latrace.html

If yes, how to uninstall it? It does not appear in Manage applications list...

apt-get purge latrace

I uninstall it alright, but when i try to activate again the dev-tracing tools, or uninstall anything else, it gives me error like cache is updating, so no possible to do anything...

Give it a reboot and don't install any development tools while the icons issue is fixed...

Will do.. fingers crossed people!
I think I will never install anything from nokia store again..

Thank to thedead1440 for the patience and as always good tips

I just hate to love this phone so much...

No no, install apps as you used to; it makes no difference and the device is there to be abused not hidden away

Do update on the icons issue though