There is sometimes a difference in the way the syllables fall in the word, which is how they're laid out in the dictionary, and the relative stress they carry within a line, which is not simply a series of words strung together. The ghost of the metric tends to pull at the metrics of the word itself, so that you will scan a word by itself one way, and (while it still scans that way as a word) it will scan differently as a part of a line. This, I believe, is why people do a lot of fighting about how to scan lines; it's the uneven pull of the scansion of the line and how a given syllable fits into the line, and how the same syllable fits into the word that gets people going. One person champions one point of view, the other person hears more of the other.
My belief is that it's the tension between the two that helps produce some of the music of a given line, how the real (syllable stress in the word) slips into the ideal (metrical stresses that are demanded by a given foot). Think of a line of single syllable words, each one theoretically stressed, yet I'd say close to impossible if not impossible to crowd a ten stress line into a ten syllable line in English metrics. The line will often go iambic, not because each of the words isn't stressed, but because the relative stresses are different and because the actual stresses we work with as writers are more subtle than we will usually admit.
The word, the line, the sentence and the meter all have different pulls on the stressing of a given line, and it's part of the art to play them all off against each other. Homing in on the number of syllables and their dictionary stressing, therefore, is not a reliable guide as to how a line is to be scanned. Is that confusing enough?
At any rate, that's what I think.