Looks like i know how that happens at least in template i'm working now. When i add new list and when i add comment for list then all variables disappeared third time for me just now.
I guess you wanted to say clean 5.0.3.1...
Yes i just uninstalled zenno with REVO and installed clean 5.0.3.1 and that problem is there.
Did you tested this and you do not have any problems with that ?