Students logging into the MyCampus system at Glasgow University yesterday after receiving Higher results were unable to register for courses.
By the afternoon, some 900 students had been able to log on, although the program was still running slowly.
Some students took to social networking sites to complain, with one stating on Twitter: "According to MyCampus I don't exist. Good one Glasgow Uni."
Last week, the system was suspended for several days for tests after similar problems. The fault was traced to a server which crashed as it was unable to deal with the volume of users.
A spokeswoman for Glasgow University said: "We apologise for the inconvenience that technical issues are causing to students. MyCampus re-opened on Wednesday morning and is now running, albeit slowly.
"Students have been able to access the system, and we would ask everyone to be patient when attempting to log on. We wholly appreciate the frustrations that the delays are causing and would again like to apologise for this."
Figures published yesterday by Ucas, the higher education admissions service, show 22,292 pupils have been accepted into a Scottish university or college, compared to 21,630 at this stage last year – an increase of 3%.