You may need to resort to using a normal warehouse. Some of these special case maps like the Arachnos Warehouse weren't designed for glowies or other objectives, they were made just for the one mission in COV that uses them. As a result, front/middle/back tend to be messed up on them and glowy placements can be off.
Otherwise, /bug it so the developers know they need to look at the map's placement spots.
Global @Twoflower / MA Creator & Pro Indie Game Developer.
Mission Architect Works: DIY Laser Moonbase (Dev Choice!), An Internship in the Fine Art of Revenge (2009 MA Award Winner!) and many more! Plus Brand New Arcs for Issue 21!
Pity. 
Thanks, though.
Also: consider floor glowies instead of wall glowies. Floor ones have to be anchored to, well, the floor. And if it's not, DEFINITELY /bug it!
Global @Twoflower / MA Creator & Pro Indie Game Developer.
Mission Architect Works: DIY Laser Moonbase (Dev Choice!), An Internship in the Fine Art of Revenge (2009 MA Award Winner!) and many more! Plus Brand New Arcs for Issue 21!
Oh, they were floor glowies. Wall glowies would've just looked wrong, based on the mission theme.
The problem seems to have gone away, however, since I switched to a regular warehouse map. Wish I hadn't had to, though. I liked the Arachnos Set 2 warehouse layout (since it doesn't have that huge room at the end that the regular ones do and which I'm so sick of).
I'm an incompetent searcher, unfortunately, so if the answer's somewhere else, I haven't been able to find it.
Anyways, in my go-throughs of my only published mission ('A Cure For Superadine?'; not very interesting - a short collection & defeat all, no custom enemies, though I think I did a decent job on the story text :P), I've found that one of the glowies is frequently (two out of the three times through the published version - but not in testing) being generated mid-air. Looks to be about the height of one of those 3-tiered warehouse racks (map is Warehouse Arachnos Set - 2), so only players who can hover or fly can reach it. Actually, a regular jump can reach it, but it interrupts because of the movement.
Anyone got any suggestions on how I might be able to tweak things to prevent that from happening?