I've got the same problem. With the iNotes interface to Lotus Notes 8.5, as well as the posting function for the University of Phoenix Web site I have problems with the iPad not recognizing the text input field for the message body. I can input in the subject line and in other fields just fine, but on those it doesn't pop the virtual keyboard. Both are "wysiwyg" editors. My partner has the same problem with his postings for school (different university).
In the UoP Web site, the relevant code is based on:
<textarea name="messageBody" cols="" rows="" value="<br/><br/><div class="signature"> --<br />
</textarea>
I assume there's something about the <textarea> tag that's messing things up, but I'm not sure why it wouldn't be supported on the iPad, but it works fine in Safari on the Mac. Anyone have any ideas?