Hi Masba. Once you reach the KL airport, you’ll be given a special pass valid for almost a month. Thereafter you’ll need to go through a medical checkup followed by submitting your passport to your university. 2-3 weeks later you’ll receive your passport with the sticker. To answer your question, no, there will be no problem because of the eVisa.
Upon entry you will be issued with a Special Pass. Your institution will submit your passport for the Student Pass endorsement once you have completed your post-arrival medical screening, and your institution has obtained the supporting letter from EMGS.