This is by far my best ghost story mainly because there were two of us who witnessed the same thing and I know it wasn't just my imagination.
I was in the Army over in Bosnia back in '96. My platoon's job was to provide security for Eagle Base, which is the main base over there. One of our guard observation posts (OPs) was on top of an old boiler plant, we had built a shack on this tower that could only be reached by climbing up two flights of ladders. The first ladder was probably about 30 feet high and led out of the main boiler room. Once you topped that there was a little landing with no lights and only a tiny greased window. There was a small conveyor belt and that was it. Everyone was scared to death of that little dark room. It felt like there was always something in the corner watching you. From that landing there was a smaller ladder (only about 10 feet high) that led to the roof. We were all scared of going up that ladder even though it was much smaller. We'd get the sensation of being chased and fear of being pulled back down into that little room. There was a large metal trap door that opened at the top. On the roof we had a little shack with a latching door. We always had 2 people on at all times, and we pulled 12-hour shifts.
Needless to say it would get extremely boring sitting up there occasionally radioing in "Farmers in field near perimeter." or "Geronimo patrol passing through sector." We were not allowed to have any reading material, but of course we all brought up magazines, books etc. and took turns between vegging and guarding. This was fine by all except with "Captain Bosnia" our nickname for the captain of the unit we were attached to. He had a habit of sneaking up on our guard posts trying to catch us in some state of goofing off.
Being the 19-20 year-old kids we were, we would shut the trap door and put a large piece of scrap metal on top so we could hear Captain Bosnia trying to sneak up on us. It would give us enough seconds to quickly stash away whatever we had and resume a cold-blooded demeanor.
One night I was duty with a guy named Monroe. We had just come on shift, and were checking out what the other had brought. Cigarettes, magazines, CDs and junk food were all tossed out on the little table there and we were in the process of figuring out who gets to sleep first and for how long. Suddenly we heard a loud clang and we scrambled to hide the "contraband". We heard 3 loud stomping footsteps outside the door, but no one called out to us. We just sat there looking at each other waiting. Usually when coming up from behind, you'd call out to the guards but no one did. Monroe called out "Who's that?" No one answered. I said something like "someone's just trying to scare us". Remember, all of us were terrified of that place anyway. After a few minutes we were finally like enough, Monroe lifted the latch and I looked out, rifle butt ready. There was no one. We went to the trap door, it was closed with the scrap metal still on top. That spooked the cr*p out of us. We went back in the shack making sure each other heard everything the same. We had both heard the clang and the footsteps. So we went back to the trap door and tried testing it out, seeing if a person could somehow close that trap door and put the metal on top. We could not do it, the scrap was just too heavy and bulky.
Neither of us slept that night! After that I would pay others to switch OPs with me whenever I'd get OP J at night.
We also had problems with our radios up there. We'd go through sometimes 3 new batteries a shift. We tried switching out radios, it didn't matter. There was even times when the frequency would change by itself. You could be on the right freq listening to the different traffic, then it'd go quiet and the radio was on a different freq. I got extra hours there because that happend to me and my NCO assumed I had fallen asleep. I know I wasn't sleeping and didn't touch the radio either. The poor commo guy practically spent the whole deployment trudging back and forth to OP J, trying to fix whatever the current problem was.

Great read for us...but I sense that you are still spooked by the experience.

Mystery that it is with location & such, you perhaps will never be able to have a proper investigation of what that was.

Yes, I can truthfully say that place still scares me.
It is too bad I can't go back to investigate. If there was ever a place I'd feel confident in finding evidence, that would be it!