After encountering this problem in two different clients, I figured this should be reported for better understanding:
First off, Microsoft considers it a best practice, starting with Windows Server 2008 to enable DNS Scavenging which is the process which will automatically clean out stale (non-recently-updated, dynamic DNS addresses). And I have used this multiple times before with great success in same-version DNS/DC environments. However it appears that at two of our clients we’ve experienced problems where static entries have been deleted. While this is not the design of DNS Scavenging, it appears that it MIGHT be an incompatibility between environments with both 2003 and 2008 DNS servers/domain controllers in the same network. Perhaps having something to do with the aging or timestamp method. However I haven’t been able to reliably reproduce it (don’t want to test in a production environment), nor find any documentation to back up this theory. But after it occurred at my second client in a mixed DNS version environment, I figured it was worth mentioning as something to watch out for.