I suggested affininy, so you could try to have an alternative to shutting down and resetting hyperthread as a test. You can set affinity to spread out the cores as efficiently as possible so to force spreading the load across both cores and see what happens.

As for the customer putting their app on another box and it runs fine...thats a different install, wonder if there are any app settings that get in the way.

This is a real-world example I had a few years ago. An oracle database was running 2 copies of a database (different data for 2 different biz units, but the same app 2x). One db was running slow, the other was fine. Vendor darn near flat refused to support app on a vm, kept insisting that we run physical. Since mgmt was not going to purchase hardware, I spend a long time playing with resources. While I was able to make some minor improvements with some settings such as hyperthread off, isolated on a host, etc. nothing ever changed dramatically. I had to press back on the app guys as to why one db seemed ok and the other did not.... After nearly a YEAR, the dba and vendor started to go through db structure and found that a table had been added to the badly running db that was not in use. After fixing that, it ran fine. Not exactly your same problem, but it can show you that the application and OS configuration can make a difference.