-uan pinyin pronunciation It seems to me that in Mandarin, two different vowel sounds are used for words whose pinyin ends with -uan.

In some words, like 全 (quán) and 元 (yuán), the vowel sounds like "oo-en" (the nucleus/coda are "ɛn" in IPA, rhymes with English "hen").

In other words, like 換/换 (huàn) and 亂/乱 (luàn), the vowel sounds like "oo-an" (the nucleus/coda are "an" in IPA, rhymes with Mandarin "安").

Does this difference really exist, or an I imagining it? If there is a distinction, what's the rule for which pronunciation to use? It seems related to the tone and the initial consonant, but I'm not sure there is a definite pattern.
There are several cases in Mandarin of multiple sounds sharing the same symbols in Pinyin, such as -uan as you've noticed, as well as -i which has multiple sounds associated with it. In the case of -uan, this final behaves differently when prefaced with the initials y-, j-, q-, and x-. As a general rule, -u, -ue, -uan, and -un behave differently when prefaced with those 4 initials and you'll see them separated  out on any pinyin chart: 



The u in these cases is actually a ü which does not exist in English and is something I struggle with myself so I'll just redirect you here.