since my post I asked skype if they knew what could be done as it seemed the problem is coming from them and here is what they told me to do:
First please try to disable plugin directly from your browser.
1. Open your web browser
2. On the toolbar you should see the Skype Add-on/extension icon.
3. Click on the icon to turn it off.
In Internet Explorer please go "Tools" > "Manage add-ons" > "Enable or
disable add-ons" > "Skype" > "Disable".
If previous steps did not help you to solve the issue, then reinstall
Skype as follows:
1. Uninstall Skype from:
Start > Settings > Control Panel > "Add or Remove Programs" (for Vista
users, Start > Settings > Control Panel > ?Programs and Features?).
2. Search for "Skype" and remove/uninstall it.
3. Download Skype from http://www.skype.com/go/download
Important: Once you start the installation process, click the "Options"
button on the installation window and untick the following two check
- Install Skype extension for Mozilla Firefox
- Install Skype add-on for Internet Explorer
And proceed with the installation as usually.
It solved the problem, the numbers stay on the web pages.
I hope this will be of use to members with similar problem in the future!