Based on the picture you provided showing the bass drum stem problem, my first idea was that those files were created in Sibelius 4 or earlier (I know I've seen that very thing happen before). My suspicions were verified upon examination of the three sib files you sent me. All three of them have notehead definitions that match the old Sib 4 template - and there was no VDL Ensemble specified either.
Unfortunately, you will not be able to ";convert"; them to 5.2.5. Only 5.1 or later files can be converted.
Your only option I see is to start with a fresh copy of the 5.2.5 Template and re-input everything in again manually. (Actually, there is another way, but I assure you that you don't want to go that route.)
Probably not the answer you wanted to hear, but now you know.