More than once lately I have come across L3 capable switches that have ip routing enabled by default even though it is not visible in the config. This has happened on every single 4500, 4900, 3560 and 3750 I have touched in the past 6 months. So I am pretty well aware that the first thing I need to do if the device is to function as a basic L2 switch is do no ip routing. However it appears that this is lost on quite a few people. I have been working at a client for a few weeks who is doing a basic core routed vlan network with dot1q trunks to each of their sites off of their Metro Ethernet WAN. The issue has nothing to to do with normal traffic but instead management traffic. If you have ip routing enabled and have also set ip default gateway your going to end up with some problems getting to the actual device to manage it. If you are not going to use a VRF for management simply do no ip routing on the device and it will work just like any other L2 only switch.
Sometimes we just dont need routing
It appears you are not alone. I came across this today and remembered your post: http://itknowledgeexchange.techtarget.com/network-technologies/no-ip-routing-was-the-answer/
Similar issue. We had good comms on the trunks just not for the native vlan. So managing the device remotely was a non-starter till we did no ip routing. If i hqd to guess they were habing sikilar issues but assumed it was the entire trunk and not just the native. That was our initial thought but testing isolated it then we beat our heads on it for a few days. Default routes and default gateways can make bad bedfellows.