Doug
The message about the old versus the new way is pretty standard and i have never known using the old way to be the cause of vlan corruption.
If you run "sh vlan" and everything looks okay then i suspect it is.
I suspect if it is intermittent you need to look at
1) Firewalls in the path
2) your routing setup - make sure your routing is stable
3) Link utilisation - are any links in the path fully utilised
4) interface drops on devices along the path
You may also want to consider cross-posting this into one of the "Unified Communications and Video" forums as after a quick search this sort of thing gets asked in those forums most frequently.
Jon