manual: expand the protocol decoder troubleshooting subsection

Expand the discussion that timing information is not required or
optional to some decoders, but essential to others (because of the very
protocol that gets interpreted). Mention that some oversampling is
typically required. Don't suggest that PD exceptions must be bugs,
incomplete configuration may be even more typical.

Separate the "you can ..." introduction from the first check list item,
to increase visibility of the entry. Existing text was not re-flown, to
reduce the diff size.