This paper presents two studies of an intervention designed to help undergraduates comprehend mathematical proofs. The intervention used multimedia resources that presented proofs with audio commentary and visual animations designed to focus attention on logical relationships. In study 1, students studied an e-Proof or a standard written proof and their comprehension was assessed in both immediate and delayed tests; the groups performed similarly at immediate test, but the e-Proof group exhibited poorer retention. Study 2 accounted for this unexpected result by using eye-movement analyses to demonstrate that participants who studied an e-Proof exhibited less processing effort when not listening to the audio commentary. We suggest that the extra support offered by e-Proofs disrupts the processes by which students organise information, and thus restricts the extent to which their new understanding is integrated with existing knowledge. We discuss the implications of these results for evaluating teaching innovations and for supporting proof comprehension.