How can there be different versions of WB?
Anyway, as DeeZire already demonstrated you can get it to work rather easily by hex editing your bse file after saving. Takes a few seconds. Make sure the header file contains the correct case sensitive name instead of the all lowercase name the WB saves it as.
For example, Castle_GondorSE got saved as castle_gondorse. When I hex edited the bse to Castle_GondorSE, my changes worked fine:
Hopefully EA will fix this, or if they don't somebody can code up a quick fix that'll correct the header for us. Like "bse <bsefile>" and it makes the correct capitalizaiton or something. Shouldn't be too hard to code, but we should wait on the patch(es) to see if EA fixes it methinks. Meanwhile hex editing works fine, and again, only takes a few seconds.
Take care.