Could well be related to an inherent feature of the game, rather than something relsated to conflicts among custom content (though would not entirely rule out that possibility).
That is to say that items have an inherent attractiveness value as to choice of use. If there are, for example, two items identical in function available, a Sim will generally (but not always) choose to use the one deemed more attractive.
By attractive, I'm not describing esthetics, but rather the qualities attached to the object itself.
There is a rough (but by no means sole) correlation between the attractivenes of any item and its price (a more expensive version will generally be more attractive to a Sim). But also one has to take into account how strongly any particular item satisfies needs. The environment score of a particular room may also come into play, all other considerations being roughly equal.
Beds, for instance, which have an energy satisfying level of 8 would be more readily chosen for use in preference to beds with an energy level of 1 were both equally accessible and available. Or if there are two beds with equal needs satisfying capabilities available, the more expensive of the two should generally be more likely to be chosen.
If you make every bed in the dorm identical in style (individual bedding can, of course, differ), then probably the dormies will be more likely to be prompted by the game to use the one in their own room.
There are also reservable beds and bed hacks available which you might find helpful at Simlogical:
http://www.simlogical.com/sl/Sims2Pages/Sims2_Sleeping.htm.