I am having the same problem, I think this is a bug in the solidworks. in my case i am not using configuration but i am using equations. there are some equations in assembly and then i further have some more equations in the part and whenever i change the value of a global variable in the assembly,technically everything should rebuild . But in my case it does not update properly. i mean assembly rebuilts well but parts dont. So to resolve that I have to open the part everytime and rebuilt the every single part in the assembly individually to get the desired results. And there is no chance that it is something wrong with my computer because i am using an 8 core workstation.........hoping for a solution from someone if there are any settings to change...........................
I don't think that it is likely to be a problem with your computer or your operating system. Others have reported that the "rebuild all configurations" doesn't seem to work. Others have also reported that equations don't update as automatically as they would like, often reuquiring two rebuilds. Since two rebuilds don't fix your issues, I doubt that it is equations that are causing the problem, although they might contribute. Does this happen with more than one part? I would send any offending parts into your VAR so that SolidWorks can get their hands on them.
Can you attach file for you problem?