It’s puzzling alright. I have a dedicated Ubuntu HTPC running with a Hauppauge HVR4000 hybrid PCI card which only runs either in DVBS or DVBT. Wasn’t easy to set up originally but it’s worked through many OS and kernel upgrades with a bit of work.
I’ve never had the need to try a VM but I imagine having your tuner work on a previously similar setup only to find the same replacement doesn’t is certainly puzzling. Might be worth starting from scratch and see what progress you make. As I don’t use a VM I can’t even do a like for like Test for you.