I know exactly what you mean.. I believe the 'hidden' prim issue as I call it, will be fixed in time at some magical upgrade.
I am not 100% sure if it is Si, Inventory severs or physics. (ODE)
I have seen it here
I have seen it in XP and Vista standalone.
I have seen it in my Linux private sandbox.
I have seen it from SVN build r5977 to SVN build r6045 and not availables
RULE #1
NEVER USE SECOND INVENTORY WHERE YOU BUILD.
make a lil corner for it or travel to Sandbox, logoff, use 'last' in Si then logon, TP home and continue building,