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The latest releases (2.4 & 2.5) of Rules breaks the 'Payment Method' configuration page. If you disable or enable any of the payment methods they disappear from the UI.
We have reproduced it on a fresh install with Commerce and Rules 2.5. Rolling Rules back to 2.3 resolved it.
Whilst it mentions Rules 2.3 on the project page, it does say that it works with the 'latest release'. It may break other sections, however we've only found this so far. We haven't found the source of this issue yet, as it took a while to track down what had caused it.