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I notice that some words have the same prefix but are pronounced differently; for example: precision, preference, prescription, etc.
Are there rules about pronunciation that you apply when you find a word you don’t know how to pronounce, or do you refer to the dictionary?
There are very few reliable rules for English pronunciation. Even something as clear as the letter 'g' being hard before an 'a', 'o' or 'u' and soft before an 'e' or an 'i' has exceptions: "gear" and "gaol" for example.
When presented with an unfamiliar word, one can make an educated guess as to its pronunciation, especially if one knows related words, or recognizes the etymology, but the only reliable way to know is to consult a dictionary.
Another example that shows how unhinged English pronunciation is from spelling is the pair of words "polish" (as is shoe polish) and "Polish" (as in a Polish mathematician). Nothing about the spelling could tell you that the letter 'o' is treated differently in those two words, because they have the same spelling!
Well, in many cases there are rules, but reading the rule closely, you usually find an "except", as in the case of the spelling rule for the dyad e and i: "I before e, except after c", to which there is an additional except, because there are a few words where e precedes i after c.
Further, the first rule, when you encounter a word you don't know how to pronounce (at least on the list I was given) is "Consult a dictionary."
Note, too, however, that there are more cases where words are pronounced differently by one set of English speakers than by other sets. Though I can't cite any examples at the moment, I frequently hear words pronounced differently by a speaker who comes from the UK than the same words are pronounced in the US.
In English, pronunciation is not always predictable, but most things do have a reason and it is worth thinking about the reason. You are right to say that these three words have the same prefix, and RegDwight is wrong to deny it: all three derive from Latin words with the prefix prae-. In English “preference” is stressed on the first syllable, which has the vowel /ɛ/. “Precision” and “prescription” have the stress on the second syllable, so the vowel in the first syllable is reduced to /ɨ/, at least in British English.
