I had this same problem: Scroll bar disappearing. I diagnosed the problem to be with the option, "Use hardware acceleration when available" found under "Tools>Options>Advanced>General". When enabled (according to the Firefox 4 documentation, this option is enabled by default) my scroll bar would disappear with Windowblinds loaded. When I unloaded Windowblinds, disabled the option in firefox (I had to unload Windowblinds first in order to see the checkbox), closed firefox, launched Windowblinds, then relaunched firefox, I no longer had a problem with my scrollbar.
The problem, therefore, appears to be an incompatibility somewhere between the DirectX/Direct3D calls made by Firefox to the Display driver (NVidia's in my case) and the way they are interpreted/handled by Windowblinds to reskin them. At least that's my best guess as to where the problem exists. Disabling the option prevents this from occurring but dies not resolve the issue of why it exists in the first place. It may be that the NV display driver simply needs to be updated. Given the many different flavors of graphics devices and drivers, your mileage may vary 
Here's what Mozilla had to say about the Hardware Acceleration feature:
"Firefox’s hardware acceleration interacts with a machine’s graphics hardware via DirectX or OpenGL, depending on platform. These interactions tend to be very sensitive to the graphics environment on the system (e.g., the specific video card(s) on the system, how much VRAM is available, the version of the video driver, the OS version, etc). In fact, there are so many permutations of the relevant factors that we can’t test them all internally." [source: http://hacks.mozilla.org/2010/09/hardware-acceleration/]
My setup:
- WinXP SP3
- Dell M620 (laptop)
- i7CPU@2.67GHz
- 4GB RAM
- nVidia NVS3100M (6.14.12.6099)
- Firefox 4
- Windowblinds 7.2 (build95 x86)
Again, YMMV, and I don't know if by disabling this option it will fix your issues, but it may be worth a try if you haven't already.
Cheers,
Joe
