In SolidWorks 2011, there is a new option in Tools > Options > System Options > Hole Wizard/Toolbox. I've taken a screenshot and highlighted the new option in yellow:
This option didn't exist prior to SolidWorks 2011, and for some people it can be a Good Thing. What it does is tell SolidWorks that whenever it finds a reference to a Toolbox part, go to this one specific folder to find the corresponding model. If you have mistakenly referenced Toolbox files from different locations, this can be an easy way to get things referenced correctly.
However, there can be a down side. IF you use Toolbox as a "part generator" to create your own library parts, then doctor them up and store them in another location (such as a regular Design Library folder on your network), this can cause a problem. You see, even though you have referenced the "custom" parts from your external library folder in your assemblies, the parts are still Toolbox parts. Also, if this new option is turned on, the next time you load your assembly, it will get the original Toolbox parts from the original Toolbox repository.
So, big deal -- don't turn on the new option. Then Toolbox will behave just as it did before 2011, right? That is correct, but the wrinkle here is that the new option is turned on by default. Since it didn't exist before 2011, there is no "old setting" to copy, so bottom line is this new option -- and this new Toolbox behavior -- is turned on for everyone in SolidWorks 2011 whether you want it or not. Not a big deal, since now you're aware of it -- it's a one-click fix. But if you missed it in the What's New, it can cause a little head-scratching. Until now, because I've just explained it to you :)