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The only change which we know of is the one that you rightly pointed out in bug http://bugs.adobe.com/jira/browse/FLEXENT-791 . There are no other behavioral changes that occur when you compile your application with automation.
With regards to your statement
Secondly I notice that using RuntimeLoader.swf on my application remove the text of some labels I have in my login form.
This does not happen when compiling the application with automation libraries.
Can you please send us a working sample of this issue as we have not come across this behavior before.
I the moment I can just send a screenshot comparing the application running normally and with the runtime loader.
I will try to send you a working simplified example of the problem.
Yes that would be great ! Thanks a lot .