so you added the depot file to the blpackage and not as a soft-link, and then deleted the original depot file.
deleting a depot file object should have nothing to do w/ the blpackage if there is no association between the two.
how are you executing the addExternalCmd commands - w/ what args, where are you getting the blpackage key, etc ? can you show the whole script or sequence of commands ?
the 'performance commands' run faster because they don't startup a jvm on each call - just a single jvm is opened (embeded in nsh) and the calls feed into that.