I pulled build 1070 from the Repository and my problem is not in that build. Perhaps this will work for you too, Anthony.
To do this, you need to build it yourselves. What I did:
I looked up a suitable build from :
https://tvheadend.org/projects/tvheadend/repository/revisions?page=4
where I saw a date where it was still working (before Jaroslav Kysela his fixes to the ECM / Descrambler code -> I picked 39b6bc1d
git clone
https://github.com/tvheadend/tvheadend
cd tvheadend/
git checkout 39b6bc1d
./Autobuild.sh (I'm running Ubuntu 14.04 - so that worked from this version on)
In your parent-directory you will now find a file called tvheadend_3.9.1070~g39b6bc1_amd64.deb
You can install this package by running
dpkg -i tvheadend_3.9.1070~g39b6bc1_amd64.deb
This will downgrade your current version to version 1070 (from 2014-07-10). This version works for me with encrypted channels fine.
Hope it works out for you as a temporary work-around.