I'm doing late course registration at the moment, and a problem I've encountered is that not all of my engineering courses show up on the undergraduate master course timetable search (link: https://adweb.cis.mcmaster.ca /mtt/index.php).
They are the following:

MATH 1H03 (Linear Algebra)
MATH 1N03 (Calculus I)

Could someone please explain to me why that is and how I might be able to work around that problem?

Hi I think you're referring to the wrong undergrad calendar. Make sure it's 08/09. These courses are no longer offered. The math courses for Eng 1 are now MATH 1Z04, 1ZZ5.

Also occasionally what will happen is that the engingeering course and the science course will be pretty much exactly the same - so the two classes are combined to be the same lecture - the same course will have two course codes.

The math courses were changed this year in engineering. It used to be math 1N03, 1NN3 and 1H03. It is now Math 1Z04 and 1ZZ5 that you will be taking.