Hi Dave,
as Jonesey said, can you describe the steps in details ?.
Also - just to note, when you load a track template and it doesn't work, do a double check to see what the actual plugin it has loaded.
At the plugin GUI pull up the VST Properties and display the path - just in case it's actually got the 32bit version loaded.
Before I got all my VST paths sorted out, this happened to me.
A 32bit plug can end up being loaded, and you would never know because it does not appear bit-bridged ... from looking at the GUI, it looks just like the 64bit plug, but checking the plugin path in the VST properties will reveal whether or not the correct file is loaded.
Problems with automation are another symptom of 32/64 plugin conflict that can happen if there's a copy of a 32bit plugin somewhere in the scan path - and sometimes they are there where and when you really don't expect it.
And as you point out, once you've tidied everything up, you need to do a VST re-scan, and recreate any templates that were affected.
Good luck and keep us posted.
Cheers - Cliff