So, I'm sure you've long since figured this out, but for posterity: the native VLAN on Cisco switches is 1, and by default tags for the native VLAN are not sentacross trunks. In general, I'd recommend that you move your production data network onto a different VLAN. Easier said than done, I know, but running data on the native VLAN is not recommended (for a number of reasons, some of which you've experienced).
HTH,
Seth