Maybe not just one school.
For better or worse MoM is going to view you in light of the school(s) you attended (or supposedly attended, as applicable) and MoM's experiences with those schools. If there has been a lot of immigration-related fraud associated with that school (or "school") then you can get ensnared even if you're the only honest student/trainee.
It's also possible MoM has concerns that you had two separate stints in Singapore. MoM simply might not want to give you a third ticket after granting two previously. It could look like the "professional student" pattern that SMS mentioned, especially if you were in a third country doing much the same thing.
You can ask MoM for more information, including how long you'll need to wait before they will consider another application. MoM has no obligation to answer, but you can try.
