I was kinda baffled by the way your other thread ended up. It is a bit less mysterious since the SolidWorks Toolbox is involved. I've heard of many different problems with it, and I know Toolbox parts behave differently than normal .sldprt files. Some users even gave up on it and went to a more home brewed toolbox system. I've also heard it has gotten better. However, I haven't used it in years. What version of SolidWorks and EPDM are you using?
If it is true that parts are being versioned (which requires check-in) without being checked-out, then something is seriously wrong. That is pretty much the failure of EPDM's reason to exist.
Is it possible users are just doing check-out-in on accident (and permissions are not set as intended)? You may need to summon a VAR. Otherwise, you would probably need to provide a lot more detail if you want help here (screenshots are helpful). When exactly are the Toolbox parts being versioned (on check-in of the assembly? only on certain change state transitions). What does the History look like on one of these components? ...But since I'm unfamiliar with the details of SW Toolbox I'm not the man for this job. Good luck.