Is the file hosted with FileMaker Server?
Has Server been updated to the latest update?
This is known to still happen if server has not been fully updated.
The file is hosted with FMS, but I have all the updates in.
FMS is on 12.03.327
Please take a look at this screen shot. It compares two portals that are identical save that one has a portal filter and the other does not. The filter expression has been pasted to the layout. This was created with FileMaker Pro 12.0v3 on a Windows XP system. I don't have a copy of server 12 to test or I'd try that to see it is a factor here.
Feel free to download and test this file for yourself and you might also test a copy of your file by opening it on your development machine with FileMaker Pro instead of the hosted copy on your server to see if that makes a difference.