This is definitely true I found for learning Chinese characters. Using Pinyin input to do everything results in character amnesia, by drilling on writing the characters makes it easier to recall them when you see them next time.
The other extreme, like at my university, is to drill writing everything (and cover less-interesting topics like telling the time, and almost useless words like '雙胞胎' - how many twins are there in China, Confucius Institute?!) I suspect most of your problem comes from trying to read isolated characters.
The issue with writing characters isn't writing individual characters. It's writing whole sentences, and then facing the inevitable error feedback from others. I get this with Pinyin too because Pinyin autocomplete often inserts the wrong character and I don't notice until it's too late, but that's just it: pinyin autocomplete kind of promotes laziness. 90% of the time it's correct, and so I don't spend a lot of time proof reading it. I have just found hand-writing slows everything down and the muscle memory aids in remembering.