All my emails are getting picked up as spam because they have a script tag in it. How can I fix that ?

If the emails going out all have the following code in them
<script charset="utf-8" id="injection_graph_func" src="chrome://skype_ff_toolbar_win/content/injection_graph_func.js">
</script>

Then that is a result of the skype toolbar mucking up the content that the wysiwyg. The easiest way to work around this is to disable the skype toolbar when using the application.

If you are running Internet Explorer 7 you can follow these instructions rather then having to turn off your Skype tool bar.

These instructions are for Internet Explorer 7.

Click on the "Tools" menu, and select "Manage Add-Ons" -> "Enable or Disable Add-Ons".
Locate the add-on named "Skype add-on (mastermind)" (or similar) and select it.
Below the add-on list, click on the "Disable" option to disable this add-on.
Click ok, and close all Internet Explorer windows.

To test that this has been successful, locate a "Contact us" page on a
website to see if Skype is still highlighting phone numbers.