Lockups in apps and general slowdowns almost sound thermal related to me; you say you've got all the latest drivers, and that the machine was playing up before the Pinnacle card went in. Correct me if wrong, but it sounds like it's getting progressively worse and especially in CPU intensive tasks like media encoding. I'd check that in the course of your various upgrades the processor heatsink hasn't been dislodged or knocked off kilter. Same for case fans, and that they're all running OK. I'd also see whether anything is obstructing airflow.
Use Motherboard Monitor to check your temps?
MBM
Maybe dismount, clean, reapply thermal gunk to HS and CPU. I wouldn't necessarily think merely using another OS will cure the problem. Anyone else got any advance on this?