I have 21 items that should load onto four factors. Several of these items had been reverse-coded. However, in a factor analysis, all the reverse coded items load onto one factor (when they actually should load onto four separate ones). I had reverse coded those items prior to running the CFA, but a previous question did suggest I am correct to do this, so what might be the issue here?
This is quite common and I have seen this many times before. The reverse-coded items share commonalities because they all share a similar methodological detail. If you measured the same construct using a self-report questionnaire and a physiological measure, for example, you would find that the self-report and physiological indices load on different factors because they are different methods, despite measuring the same construct. I would simply explain the reverse-worded factor as it is, a factor comprised of the items that are reverse-worded because these items share a similar response pattern.
Edit: I will also mention that reverse-coding items should not matter. If the items are reverse-worded, while the rest of the items are worded straightforwardly, the items that are reverse-worded will likely correlate strongly simply due to their reverse-worded nature.