We had 5 tame wolves sitting in a house on a Survival Bukkit-Server, they seem to have disappeared sometime after the update to 1.4.2. Another wolf was tamed and brought to the house but disappeared over night.
No further bugtesting was done before issueing the report.
If you can repeat this on vanilla, make another ticket. As you're using a server modification, the bug could be a bukkit bug. Closing this as invalid.