Well i can tell you i don't think you are crazy. I have a Bogner Unerschall and i have yet to get it to play nice. My setup is a little different, i have the Pro running into a dt50 but the noise is just insane. I wondered if it was a gain stage issue of some sort but everything i have tried has been useless to get rid of it. Everything you stated seems to be the same for me. Whether I run it in the FX loop or i run my guitar into the pedal then into the POD the results are the same. If i run it straight into the DT50 without the POD no noise.
I finally just took it out of the rig, did'nt want to fight it anymore. I'm happy with the sounds i can get without it but i realize everyones needs are different.
I know this doesn't help much besides to say i think it's not so much an error in settings as it is these pedals hating Pod HDs lol. I may sit down again with it tomorrow see if i can come up with anything. If I discover anything ill post.