I have the exact same problem but it only began once I had it tuned- i used Tom (most people on here do) and an Excalibur 2 tuner. I tried to troubleshoot this with him but we never fixed it. I chocked it up to being a peril of remote tuning and figured I'd dyno it if I really wanted to fix it.
Please let me know what the issue was when you solve it... I'd be most interested to know.
2009 Focus Coupe SES 5-spd MTX
Steeda STS, Steeda SRI, FSWerks Race header, 2.5" flex, and 2.5" race exhaust
Tuned by Focus-Power (Tom)