If you write you canvas app in such a way that it invokes JavaScript function via the href attribute as follows:
<a href="javascript:myfunc();" >click here</a>
then I would you to check your app to see if it still functions as expected.
Recently, I found that the above method may fail in some canvas pages (though it is working perfectly if it is running as a web page by itself).
To rectify the problem, you can simply rewrite the above code in the following way:
<a href="#" onclick="myfunc();">
Hope this helps.