I have the same problem 669 and @IvaRo has refered me to this topic so I will continue here.
I did the Base64 decoding and put the decoded version as the new index.php. It didn't help to get rid of the <? on the beginning of the html but it did remove the <? on the end of html.
Please note that this symptom happened even if I make a fresh installation extracted from original Pulse 4.7 ZIP file. In the example above I just trimmed the layout.php to make it short and simple.
It is worth to mention that the extra chars don't appear on the admin page:
I also notice that @eltoron 's website above still having this issue. This is what I got when viewing the source:
My server is still under testing so it lies behind a firewall and cannot be accessed from Internet. The users mostly using IE and not very happy with this, hope we can have a solution soon. Thanks.