I am at 45 repair and I wanted to repair ED-E so I used 2 Fixin' Things magazines to get to 65. it only went to 55. What gives?

Only one magazine will give you a boost at a time. Take the Comprehension perk at level 4 and they give you a boost of 20, along with skill books being worth and increase of 4.

They should be able to stack imo.
See little point to use them cause of the tiny bonus.
Retention perk should at least do this: fist skill mag +10, second skill mag +5, third skill mag +5 etc.
So that with enough skill magazines I could get a skill up to 100 for a short time.