Chemical phenomena can be described using three representation modes: macro, submicro, and symbolic. The way students use and connect these modes when solving conceptual problems was studied, using a think-aloud interview protocol. The protocol was validated through interviews with six faculty members, and then applied to four graduate and six undergraduate chemistry students. We used a "levels of complexity" framework to analyse responses: the macro and symbolic modes were considered system-level representations, and the submicro mode a component-level representation. We found that faculty members thought of system-level properties as emerging from mechanistic interactions between particles on the component level--an emergent perspective. In many cases, the students either failed to connect the system and component levels, or thought of system-level properties as guiding the behaviour of particles on the component level--a "submergent" perspective. Some students used their familiarity with a symbolic equation describing the behaviour of a substance as the starting point of a thought process that leads them to impose mechanistically unwarrantable behaviour upon its particles. We concluded that a submergent perspective inhibits students from confronting their misconceptions regarding particle behaviour, and explains why students are often able to correctly solve algorithmic problems while failing to solve conceptual ones. It is suggested that the directionality of connecting particle behaviour to system-level properties should be emphasized in teaching. (Contains 3 figures and 3 notes.)