We've recently upgraded from CS3 to CS5.5. I have recreated the ouput modules and set my defaults as per usual (I have specifically created an output module for Quicktime Avid 1:1 and saved it with a new name). Everything works as usual untill I quit After Effects, When I start up again this saved module has disappeared and ALL the defaults settings (movie, frame etc) defaults to the next in the list. So if RAM preview was previously set to Lossless, it becomes Lossless with Alpha etc and my created module isn't there anymore. If I specifically save these settings it doesn't make any difference. And if I manually load this, I still have to set the defaults for movie, frame etc to what I want.
I've searched help and the forums, but are not finding a sollution.
It sounds like your preferences files are corrupted. What's your system? What OS? Have you tried deleting the preferences file? I've never had any problem saving templates.
I'm running Windows 7. I did reset the preferences. I even followed your link to make sure I did it correctly, but the problem persists. Upon further invesitgation I noticed that the default output modules have also changed without me editing them. I included some pictures to show what I mean. Happily when I reset the preferences these return to normal.