I was experiencing similar issues with Flash videos when I had my two radeon HD 5850's in my system as well. From my understanding, it was related to the GPU varying between idle, 2D, and 3D clock speeds. The speeds are dropping down too low, causing the GPU to underperform, as a result, jerky / lagging Flash playback.
This is caused by the energy saving feature built into the graphics card (and also what seems to be an on-going issue on Adobe Flash's end). One method of fixing this is disabled ULPS (Ultra-Low Power State).
The "issue' regarding about seeing your GPU frequencies at 400 / 1000 MHz is normal. When you connect multiple monitors to your system, the graphics card needs to run at higher speeds to drive the two displays. I mean, it needs to churn out all the pixels for two monitors instead of one.
FX-8350 @ 4.8GHz // ASUS Crosshair V Formula 990FX // Sapphire Vapor-X HD 7970 + Dual-X HD 7970 // Thermaltake Frio w/ push-pull (using Antec Formula 7 Nano-Diamond + Cooler Master JetFlo fans) // 8GB (2 X 4GB) G.Skill RipJawsX 2133MHz // Corsair TX850 850W // Corsair Force GT 120GB SSD (OS) // Kingston V200+ 120GB SSD // WD Caviar Black 1TB // Windows 7 Ult x64