せい is obviously more common as a kanji and radical reading but there are still a few しょう’s that trip me up
せい；正義、正解、整理、政府
しょう：正直、正月、証人、症状
Is there some etymological hint or is it just one of those 'gotta learn ‘em’ situations?
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The etymological reason is usually “these words were borrowed from Chinese in one period, and these other words were borrowed in a different period when Chinese pronunciation had changed”, but that isn’t any use for guessing the reading of a word.
In this case しょう is the Go-on 呉音 (4–6th century, Wu Dynasty pronunciation), and せい is the
Kan-on 漢音 (7–9th century Han Dynasty pronunciation).
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Sometimes that is useful when one reading is common and the other is only used in like Buddhism-related words. But yeah, not really helpful for 正.
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Love the extra info, thanks!
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My general recommendation would be to practice other words containing kanji you’re having trouble with.
However, from the ones you mentioned
- 正直 - extremely common word. You’ll get used to the reading by reading more. It’s still giving me some trouble as well.
- 証人、症状 - both use only しょう
- 政府 - contains 政 which is related to politics so you can learn a couple more politics-oriented words
- 正義、正解 - also very common words. First one appears a hell lot in shounen anime, the second one in manga, novels, etc.
The only problematic ones I can think of are 整理 and 正月. The latter you can practice by reading articles about the New Year 
.
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