Practice, practice, practice...retrain your brain.
A learning disability is not a learning impossibility. You have to want it enough to keep trying until it becomes burned into your subconscious by repetition. Your body can learn things on an organic level, even if your intellect refuses to participate in the process. Eventually you'll be able to tie your shoes in the dark, because your fingers will know the movements, even when your eyes can't see what they're doing.
In the case of clock-reading, look for a watch that has both the hour designations and the minute numbers on the same face. Wear that for a year and see if you don't pick it up after a while. Or take a compass, draw a bunch of blank circles and fill in the numbers yourself (looking at a clock for reference), until you have the digits and their positions all memorized.
It helps to start, by remembering that each quarter of the circle, during an hour, represents 15 minutes: 15 (quarter past)...30 (half past)...45 (three quarters/quarter 'til)...60.
Within each 15 minute block, are three groups of 5 minutes each. After that, it's pretty simple, you just count by ones.
I learned to tell time on a standard clock face, but when I got my first job in radio, I had to keep logs in Military time and it confused the hell out of me at first.
You'll get it - just be persistent.